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UniProtKB - P0AAR3 (YBAK_ECOLI)

Entry version 117 (07 Apr 2021)
Sequence version 1 (11 Oct 2005)
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Protein

Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK

Gene

ybaK

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Functions in trans to edit the amino acid from incorrectly charged Cys-tRNA(Pro) via a Cys-tRNA(Pro) deacylase activity. May compensate for the lack of Cys-tRNA(Pro) editing by ProRS. Is also able to deacylate Cys-tRNA(Cys), and displays weak deacylase activity in vitro against Gly-tRNA(Gly), as well as, at higher concentrations, some other correctly charged tRNAs. Unlike some of its orthologs it is not able to remove the amino acid moiety from incorrectly charged Ala-tRNA(Pro).2 Publications

Miscellaneous

Has been suggested to be potentially involved in suppression of transcription of ushA.
Reaction mechanism involves exclusion of catalytic water from the active site and substrate-mediated catalysis: the sulfhydryl side chain of the Cys substrate acts as a nucleophile and attacks the carbonyl center of the ester bond, leading to the cleavage of the Cys-tRNA ester bond and formation of a cyclic cysteine thiolactone intermediate. In contrast, the INS editing domain of ProRS catalyzes Ala-tRNA(Pro) hydrolysis via nucleophilic attack by a catalytic water molecule (PubMed:23185990).1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei29Participates in proton transfer during catalysis1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

  • response to X-ray Source: EcoCyc
  • translation Source: UniProtKB-KW
Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionLyase
Biological processProtein biosynthesis

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG12454-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK (EC:4.2.-.-)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:ybaK
Ordered Locus Names:b0481, JW0470
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Non-essential gene.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi30G → C, I or V: >100-fold decrease in Cys-tRNA(Pro) deacylation activity. Fails to gain Ala-tRNA(Pro) deacylation activity. 1 Publication1
Mutagenesisi136D → A or C: 6-fold decrease in Cys-tRNA(Pro) deacylation activity. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001686201 – 159Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaKAdd BLAST159

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P0AAR3

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P0AAR3

PRoteomics IDEntifications database

More...PRIDEi		P0AAR3

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">Interaction</a>' section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4263284, 32 interactors

Database of interacting proteins

More...DIPi		DIP-48133N

Protein interaction database and analysis system

More...IntActi		P0AAR3, 17 interactors

STRING: functional protein association networks

More...STRINGi		511145.b0481

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1159
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P0AAR3

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P0AAR3

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the prolyl-tRNA editing family. YbaK/EbsC subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG2606, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_094875_1_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P0AAR3

Database for complete collections of gene phylogenies

More...PhylomeDBi		P0AAR3

Family and domain databases

Conserved Domains Database

More...CDDi		cd00002, YbaK_deacylase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.90.960.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR004369, Prolyl-tRNA_editing_YbaK/EbsC
IPR036754, YbaK/aa-tRNA-synt-asso_dom_sf
IPR007214, YbaK/aa-tRNA-synth-assoc-dom

Pfam protein domain database

More...Pfami		View protein in Pfam
PF04073, tRNA_edit, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF006181, EbsC_YbaK, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF55826, SSF55826, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00011, YbaK_EbsC, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P0AAR3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTPAVKLLEK NKISFQIHTY EHDPAETNFG DEVVKKLGLN PDQVYKTLLV 
        60         70         80         90        100
AVNGDMKHLA VAVTPVAGQL DLKKVAKALG AKKVEMADPM VAQRSTGYLV 
       110        120        130        140        150
GGISPLGQKK RLPTIIDAPA QEFATIYVSG GKRGLDIELA AGDLAKILDA 

KFADIARRD
Length:159
Mass (Da):17,093
Last modified:October 11, 2005 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i45CD6A2226F2AA01
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
U82664 Genomic DNA Translation: AAB40235.1
U00096 Genomic DNA Translation: AAC73583.1
AP009048 Genomic DNA Translation: BAE76260.1
X03895 Genomic DNA No translation available.

Protein sequence database of the Protein Information Resource

More...PIRi		H64778

NCBI Reference Sequences

More...RefSeqi		NP_415014.1, NC_000913.3
WP_000186631.1, NZ_STEB01000007.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC73583; AAC73583; b0481
BAE76260; BAE76260; BAE76260

Database of genes from NCBI RefSeq genomes

More...GeneIDi		58462794
947083

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW0470
eco:b0481

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|511145.12.peg.501

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82664 Genomic DNA Translation: AAB40235.1
U00096 Genomic DNA Translation: AAC73583.1
AP009048 Genomic DNA Translation: BAE76260.1
X03895 Genomic DNA No translation available.
PIRiH64778
RefSeqiNP_415014.1, NC_000913.3
WP_000186631.1, NZ_STEB01000007.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2DXAX-ray1.58A1-159[»]
SMRiP0AAR3
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4263284, 32 interactors
DIPiDIP-48133N
IntActiP0AAR3, 17 interactors
STRINGi511145.b0481

Proteomic databases

jPOSTiP0AAR3
PaxDbiP0AAR3
PRIDEiP0AAR3

Genome annotation databases

EnsemblBacteriaiAAC73583; AAC73583; b0481
BAE76260; BAE76260; BAE76260
GeneIDi58462794
947083
KEGGiecj:JW0470
eco:b0481
PATRICifig|511145.12.peg.501

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB2348

Phylogenomic databases

eggNOGiCOG2606, Bacteria
HOGENOMiCLU_094875_1_1_6
InParanoidiP0AAR3
PhylomeDBiP0AAR3

Enzyme and pathway databases

BioCyciEcoCyc:EG12454-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0AAR3

Protein Ontology

More...PROi		PR:P0AAR3

Family and domain databases

CDDicd00002, YbaK_deacylase, 1 hit
Gene3Di3.90.960.10, 1 hit
InterProiView protein in InterPro
IPR004369, Prolyl-tRNA_editing_YbaK/EbsC
IPR036754, YbaK/aa-tRNA-synt-asso_dom_sf
IPR007214, YbaK/aa-tRNA-synth-assoc-dom
PfamiView protein in Pfam
PF04073, tRNA_edit, 1 hit
PIRSFiPIRSF006181, EbsC_YbaK, 1 hit
SUPFAMiSSF55826, SSF55826, 1 hit
TIGRFAMsiTIGR00011, YbaK_EbsC, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiYBAK_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P0AAR3
Secondary accession number(s): P37175, P77281, Q2MBU6
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 11, 2005
Last sequence update: October 11, 2005
Last modified: April 7, 2021
This is version 117 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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