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Protein

tRNA(fMet)-specific endonuclease VapC

Gene

vapC

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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 site-specific 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. Expression also activates translation initiation at correctly positioned elongator codons (AAA and to a lesser extent AAG).
Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity.

Cofactori

Mg2+Curated

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

BioCyciSENT99287:GCTI-3053-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
Ordered Locus Names:STM3033
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi7 – 71D → A: No inhibition of cell growth, no degradation of tRNA(fMet). 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 132132tRNA(fMet)-specific endonuclease VapCPRO_0000410980Add
BLAST

Expressioni

Inductioni

Induced by amino acid starvation and by chloramphenicol treatment.1 Publication

Interactioni

Subunit structurei

Forms a complex with antitoxin VapB.Curated

Protein-protein interaction databases

STRINGi99287.STM3033.

Structurei

3D structure databases

ProteinModelPortaliQ8ZM86.
ModBaseiSearch...
MobiDBiSearch...

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

HOGENOMiHOG000121274.
KOiK18828.
OMAiVMSAITY.
OrthoDBiEOG6ZWJH4.
PhylomeDBiQ8ZM86.

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]
SMARTiSM00670. PINc. 1 hit.
[Graphical view]
SUPFAMiSSF88723. SSF88723. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8ZM86-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKFMLDTNT CIFTIKNKPE HIRERFNLNT SRMCISSITL MELIYGAEKS
60 70 80 90 100
LAPERNLAVV EGFISRLEVL DYDTQAAIHT GQIRAELARK GTPVGPYDQM
110 120 130
IAGHAGSRGL VVVTNNLREF ERIPGIRIED WC
Length:132
Mass (Da):14,938
Last modified:March 1, 2002 - v1
Checksum:i4AA4120DAD6B6057
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL21909.1.
RefSeqiNP_461950.1. NC_003197.1.
WP_000911336.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL21909; AAL21909; STM3033.
GeneIDi1254556.
KEGGistm:STM3033.
PATRICi32384803. VBISalEnt20916_3211.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL21909.1.
RefSeqiNP_461950.1. NC_003197.1.
WP_000911336.1. NC_003197.1.

3D structure databases

ProteinModelPortaliQ8ZM86.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM3033.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL21909; AAL21909; STM3033.
GeneIDi1254556.
KEGGistm:STM3033.
PATRICi32384803. VBISalEnt20916_3211.

Phylogenomic databases

HOGENOMiHOG000121274.
KOiK18828.
OMAiVMSAITY.
OrthoDBiEOG6ZWJH4.
PhylomeDBiQ8ZM86.

Enzyme and pathway databases

BioCyciSENT99287:GCTI-3053-MONOMER.

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]
SMARTiSM00670. PINc. 1 hit.
[Graphical view]
SUPFAMiSSF88723. SSF88723. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LT2 / SGSC1412 / ATCC 700720.
  2. "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, INDUCTION, EXPRESSION IN E.COLI.
    Strain: LT2 / SGSC1412 / ATCC 700720.
  3. "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, MUTAGENESIS OF ASP-7.
    Strain: LT2 / SGSC1412 / ATCC 700720.

Entry informationi

Entry nameiVAPC_SALTY
AccessioniPrimary (citable) accession number: Q8ZM86
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: March 1, 2002
Last modified: July 22, 2015
This is version 67 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.