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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: 4 out of 5-Experimental evidence at protein leveli

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei29 – 291Participates in proton transfer during catalysis

GO - Molecular functioni

  • aminoacyl-tRNA editing activity Source: UniProtKB
  • Cys-tRNA(Pro) hydrolase activity Source: EcoCyc
  • lyase activity Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Protein biosynthesis

Enzyme and pathway databases

BioCyciEcoCyc:EG12454-MONOMER.
ECOL316407:JW0470-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK (EC:4.2.-.-)
Gene namesi
Name:ybaK
Ordered Locus Names:b0481, JW0470
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12454. ybaK.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Non-essential gene.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi30 – 301G → C, I or V: >100-fold decrease in Cys-tRNA(Pro) deacylation activity. Fails to gain Ala-tRNA(Pro) deacylation activity. 1 Publication
Mutagenesisi136 – 1361D → A or C: 6-fold decrease in Cys-tRNA(Pro) deacylation activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 159159Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaKPRO_0000168620Add
BLAST

Proteomic databases

PaxDbiP0AAR3.
PRIDEiP0AAR3.

Interactioni

Protein-protein interaction databases

BioGridi4263284. 15 interactions.
DIPiDIP-48133N.
IntActiP0AAR3. 17 interactions.
MINTiMINT-1228144.
STRINGi511145.b0481.

Structurei

Secondary structure

1
159
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 108Combined sources
Beta strandi16 – 194Combined sources
Helixi32 – 376Combined sources
Turni41 – 433Combined sources
Beta strandi44 – 529Combined sources
Beta strandi55 – 6511Combined sources
Beta strandi68 – 703Combined sources
Helixi72 – 798Combined sources
Beta strandi84 – 863Combined sources
Helixi89 – 968Combined sources
Beta strandi105 – 1073Combined sources
Beta strandi114 – 1174Combined sources
Helixi118 – 1225Combined sources
Beta strandi126 – 1327Combined sources
Beta strandi135 – 1395Combined sources
Helixi141 – 1488Combined sources
Beta strandi151 – 1533Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DXAX-ray1.58A1-159[»]
ProteinModelPortaliP0AAR3.
SMRiP0AAR3. Positions 1-158.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AAR3.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108Z66. Bacteria.
COG2606. LUCA.
HOGENOMiHOG000262090.
InParanoidiP0AAR3.
KOiK03976.
OMAiFTVHAYD.
OrthoDBiEOG6XDH1K.
PhylomeDBiP0AAR3.

Family and domain databases

Gene3Di3.90.960.10. 1 hit.
InterProiIPR004369. Prolyl-tRNA_editing_YbaK/EbsC.
IPR007214. YbaK/aa-tRNA-synth-assoc-dom.
[Graphical view]
PfamiPF04073. tRNA_edit. 1 hit.
[Graphical view]
PIRSFiPIRSF006181. EbsC_YbaK. 1 hit.
SUPFAMiSSF55826. SSF55826. 1 hit.
TIGRFAMsiTIGR00011. YbaK_EbsC. 1 hit.

Sequencei

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
Checksum:i45CD6A2226F2AA01
GO

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_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73583; AAC73583; b0481.
BAE76260; BAE76260; BAE76260.
GeneIDi947083.
KEGGiecj:JW0470.
eco:b0481.
PATRICi32116119. VBIEscCol129921_0501.

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_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DXAX-ray1.58A1-159[»]
ProteinModelPortaliP0AAR3.
SMRiP0AAR3. Positions 1-158.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263284. 15 interactions.
DIPiDIP-48133N.
IntActiP0AAR3. 17 interactions.
MINTiMINT-1228144.
STRINGi511145.b0481.

Proteomic databases

PaxDbiP0AAR3.
PRIDEiP0AAR3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73583; AAC73583; b0481.
BAE76260; BAE76260; BAE76260.
GeneIDi947083.
KEGGiecj:JW0470.
eco:b0481.
PATRICi32116119. VBIEscCol129921_0501.

Organism-specific databases

EchoBASEiEB2348.
EcoGeneiEG12454. ybaK.

Phylogenomic databases

eggNOGiENOG4108Z66. Bacteria.
COG2606. LUCA.
HOGENOMiHOG000262090.
InParanoidiP0AAR3.
KOiK03976.
OMAiFTVHAYD.
OrthoDBiEOG6XDH1K.
PhylomeDBiP0AAR3.

Enzyme and pathway databases

BioCyciEcoCyc:EG12454-MONOMER.
ECOL316407:JW0470-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AAR3.
PROiP0AAR3.

Family and domain databases

Gene3Di3.90.960.10. 1 hit.
InterProiIPR004369. Prolyl-tRNA_editing_YbaK/EbsC.
IPR007214. YbaK/aa-tRNA-synth-assoc-dom.
[Graphical view]
PfamiPF04073. tRNA_edit. 1 hit.
[Graphical view]
PIRSFiPIRSF006181. EbsC_YbaK. 1 hit.
SUPFAMiSSF55826. SSF55826. 1 hit.
TIGRFAMsiTIGR00011. YbaK_EbsC. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Nucleotide sequence and transcriptional analysis of the E. coli ushA gene, encoding periplasmic UDP-sugar hydrolase (5'-nucleotidase): regulation of the ushA gene, and the signal sequence of its encoded protein product."
    Burns D.M., Beacham I.R.
    Nucleic Acids Res. 14:4325-4342(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 149-159.
  5. Jimenez S., Bairoch A.
    Unpublished observations (AUG-1994)
    Cited for: IDENTIFICATION.
  6. "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography."
    Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.
    Electrophoresis 20:2181-2195(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: B / BL21.
  7. Cited for: LACK OF EDITING ACTIVITY ON MISCHARGED ALA-TRNA(PRO).
  8. "The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase."
    Ruan B., Soll D.
    J. Biol. Chem. 280:25887-25891(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A DEACYLASE, SUBSTRATE SPECIFICITY, DISRUPTION PHENOTYPE.
  9. "Aminoacyl-tRNA substrate and enzyme backbone atoms contribute to translational quality control by YbaK."
    Kumar S., Das M., Hadad C.M., Musier-Forsyth K.
    J. Phys. Chem. B 117:4521-4527(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, REACTION MECHANISM, MUTAGENESIS OF GLY-30 AND ASP-136.
  10. "Crystal structure of trans editing enzyme ProX from E.coli."
    RIKEN structural genomics initiative (RSGI)
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.58 ANGSTROMS).

Entry informationi

Entry nameiYBAK_ECOLI
AccessioniPrimary (citable) accession number: P0AAR3
Secondary accession number(s): P37175, P77281, Q2MBU6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2005
Last sequence update: October 11, 2005
Last modified: July 6, 2016
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.