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Protein

tRNA(fMet)-specific endonuclease VapC

Gene

vapC

Organism
Shigella flexneri
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Toxic component of a toxin-antitoxin (TA) module. A tRNA-(fMet) endonuclease, it cleaves both charged and uncharged tRNA-(fMet) between positions 38 and 39 at the anticodon stem-loop boundary. Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His), tRNA(Leu), tRNA(Phe) tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression in E.coli inhibits translation, leads to loss of cell growth and degradation of tRNA(fMet); these effects are neutralized by expression of cognate antitoxin VapB. The VapB/VapC complex probably regulates transcription of its own promoter.
Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity.

Cofactori

Mg2+Curated

Enzyme regulationi

Inhibited by EDTA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi7 – 71MagnesiumSequence analysis
Metal bindingi98 – 981MagnesiumSequence analysis

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Toxin

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciRETL1328306-WGS:GSTH-5023-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA(fMet)-specific endonuclease VapC (EC:3.1.-.-)
Alternative name(s):
RNase VapC
Toxin VapC
Gene namesi
Name:vapC
Synonyms:mvpA, stborf2
Ordered Locus Names:CP0245
Encoded oniPlasmid pCP3011 Publication
Plasmid pMYSH60004 Publications
Plasmid pWR1001 Publication
OrganismiShigella flexneri
Taxonomic identifieri623 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeShigella
Proteomesi
  • UP000001006 Componenti: Plasmid pCP301

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 132132tRNA(fMet)-specific endonuclease VapCPRO_0000410981Add
BLAST

Proteomic databases

PaxDbiO06662.
PRIDEiO06662.

Expressioni

Inductioni

Degradation of tRNA(fMet) is induced by chloramphenicol treatment, suggesting the antitoxin is unstable.1 Publication

Interactioni

Subunit structurei

Forms a hetero-octomer (4 VapB and 4 VapC) complex with antitoxin VapB. The complex binds 2 different sites in the vapBC promoter, probably via VapB dimerization.2 Publications

Protein-protein interaction databases

STRINGi198214.CP0245.

Structurei

Secondary structure

1
132
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 63Combined sources
Helixi8 – 169Combined sources
Helixi20 – 289Combined sources
Turni29 – 313Combined sources
Beta strandi32 – 365Combined sources
Helixi37 – 4913Combined sources
Helixi53 – 6412Combined sources
Beta strandi67 – 704Combined sources
Helixi74 – 9017Combined sources
Helixi96 – 10712Combined sources
Beta strandi111 – 1133Combined sources
Helixi117 – 1204Combined sources
Beta strandi128 – 1303Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TNDX-ray2.70A/C/E/G1-132[»]
5ECDX-ray1.75A/B2-132[»]
5ECWX-ray1.94A/B2-132[»]
5ED0X-ray2.10A/B/C/D/E/F/G/H/I/J/K/L2-132[»]
ProteinModelPortaliO06662.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO06662.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini5 – 131127PINcAdd
BLAST

Sequence similaritiesi

Belongs to the PINc/VapC protein family.Curated
Contains 1 PINc domain.Curated

Phylogenomic databases

eggNOGiENOG4105M0J. Bacteria.
COG1487. LUCA.
HOGENOMiHOG000121274.
KOiK18828.
OMAiFELWYGV.
OrthoDBiEOG6ZWJH4.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00265. VapC_Nob1.
InterProiIPR002716. PIN_dom.
IPR029060. PIN_domain-like.
IPR022907. VapC_family.
[Graphical view]
PfamiPF01850. PIN. 1 hit.
[Graphical view]
SUPFAMiSSF88723. SSF88723. 1 hit.

Sequencei

Sequence statusi: Complete.

O06662-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKFMLDTNI CIFTIKNKPA SVRERFNLNQ GKMCISSVTL MELIYGAEKS
60 70 80 90 100
QMPERNLAVI EGFVSRIDVL DYDAAAATHT GQIRAELARQ GRPVGPFDQM
110 120 130
IAGHARSRGL IIVTNNTREF ERVGGLRTED WS
Length:132
Mass (Da):14,817
Last modified:July 1, 1997 - v1
Checksum:i4C64DB25249C2B70
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82621 Genomic DNA. Translation: AAB58157.1.
AL391753 Genomic DNA. Translation: CAC05862.1.
AF386526 Genomic DNA. Translation: AAL72335.1.
RefSeqiNP_085412.1. NC_002698.1.
NP_858378.1. NC_004851.1.
WP_000911311.1. NZ_JTBI01000002.1.
YP_009062544.1. NC_024996.1.

Genome annotation databases

EnsemblBacteriaiAAL72335; AAL72335; SF_p0245.
GeneIDi1238038.
876621.
KEGGipg:20467620.
pg:876621.
sfl:CP0245.
PATRICi18722830. VBIShiFle86970_5506.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82621 Genomic DNA. Translation: AAB58157.1.
AL391753 Genomic DNA. Translation: CAC05862.1.
AF386526 Genomic DNA. Translation: AAL72335.1.
RefSeqiNP_085412.1. NC_002698.1.
NP_858378.1. NC_004851.1.
WP_000911311.1. NZ_JTBI01000002.1.
YP_009062544.1. NC_024996.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TNDX-ray2.70A/C/E/G1-132[»]
5ECDX-ray1.75A/B2-132[»]
5ECWX-ray1.94A/B2-132[»]
5ED0X-ray2.10A/B/C/D/E/F/G/H/I/J/K/L2-132[»]
ProteinModelPortaliO06662.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198214.CP0245.

Proteomic databases

PaxDbiO06662.
PRIDEiO06662.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL72335; AAL72335; SF_p0245.
GeneIDi1238038.
876621.
KEGGipg:20467620.
pg:876621.
sfl:CP0245.
PATRICi18722830. VBIShiFle86970_5506.

Phylogenomic databases

eggNOGiENOG4105M0J. Bacteria.
COG1487. LUCA.
HOGENOMiHOG000121274.
KOiK18828.
OMAiFELWYGV.
OrthoDBiEOG6ZWJH4.

Enzyme and pathway databases

BioCyciRETL1328306-WGS:GSTH-5023-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO06662.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00265. VapC_Nob1.
InterProiIPR002716. PIN_dom.
IPR029060. PIN_domain-like.
IPR022907. VapC_family.
[Graphical view]
PfamiPF01850. PIN. 1 hit.
[Graphical view]
SUPFAMiSSF88723. SSF88723. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Plasmid maintenance functions of the large virulence plasmid of Shigella flexneri."
    Radnedge L., Davis M.A., Youngren B., Austin S.J.
    J. Bacteriol. 179:3670-3675(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: YSH6000 / Serotype 2a.
    Plasmid: pMYSH6000
  2. "The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri."
    Buchrieser C., Glaser P., Rusniok C., Nedjari H., d'Hauteville H., Kunst F., Sansonetti P.J., Parsot C.
    Mol. Microbiol. 38:760-771(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: M90T / Serotype 5a.
    Plasmid: pWR100
  3. "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157."
    Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y.
    , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.
    Nucleic Acids Res. 30:4432-4441(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 301 / Serotype 2a.
    Plasmid: pCP301
  4. "Ectopic production of VapCs from Enterobacteria inhibits translation and trans-activates YoeB mRNA interferase."
    Winther K.S., Gerdes K.
    Mol. Microbiol. 72:918-930(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TOXIN, EXPRESSION IN E.COLI.
    Strain: YSH6000 / Serotype 2a.
    Plasmid: pMYSH6000
  5. "Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA."
    Winther K.S., Gerdes K.
    Proc. Natl. Acad. Sci. U.S.A. 108:7403-7407(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TOXIN, FUNCTION AS A TRNA ENDONUCLEASE, SUBSTRATE SPECIFICITY, ENZYME REGULATION, SUBUNIT, INDUCTION.
    Strain: YSH6000 / Serotype 2a.
    Plasmid: pMYSH6000
  6. "Crystal structure of the VapBC toxin-antitoxin complex from Shigella flexneri reveals a hetero-octameric DNA-binding assembly."
    Dienemann C., Boggild A., Winther K.S., Gerdes K., Brodersen D.E.
    J. Mol. Biol. 414:713-722(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS), INTERACTION WITH VAPB, SUBUNIT.
    Strain: YSH6000 / Serotype 2a.
    Plasmid: pMYSH6000

Entry informationi

Entry nameiVAPC_SHIFL
AccessioniPrimary (citable) accession number: O06662
Secondary accession number(s): Q7BCI3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: July 1, 1997
Last modified: May 11, 2016
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Plasmid

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.