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Protein

tRNA(fMet)-specific endonuclease VapC

Gene

vapC

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Toxic component of a type II toxin-antitoxin (TA) system. 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)DescriptionActionsGraphical viewLength
Metal bindingi7MagnesiumSequence analysis1
Metal bindingi98MagnesiumSequence analysis1

GO - Molecular functioni

Keywordsi

Molecular functionEndonuclease, Hydrolase, Nuclease
Biological processToxin-antitoxin system
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyciSENT99287:G1FZD-3065-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi7D → A: No inhibition of cell growth, no degradation of tRNA(fMet). 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004109801 – 132tRNA(fMet)-specific endonuclease VapCAdd BLAST132

Proteomic databases

PaxDbiQ8ZM86

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
SMRiQ8ZM86
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini5 – 131PINcAdd BLAST127

Sequence similaritiesi

Belongs to the PINc/VapC protein family.Curated

Phylogenomic databases

eggNOGiENOG4105M0J Bacteria
COG1487 LUCA
HOGENOMiHOG000121274
KOiK18828
OMAiLDTNACI
PhylomeDBiQ8ZM86

Family and domain databases

HAMAPiMF_00265 VapC_Nob1, 1 hit
InterProiView protein in InterPro
IPR029060 PIN-like_dom_sf
IPR002716 PIN_dom
IPR022907 VapC_family
PfamiView protein in Pfam
PF01850 PIN, 1 hit
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_003197.2
WP_000911336.1, NC_003197.2

Genome annotation databases

EnsemblBacteriaiAAL21909; AAL21909; STM3033
GeneIDi1254556
KEGGistm:STM3033
PATRICifig|99287.12.peg.3211

Similar proteinsi

Entry informationi

Entry nameiVAPC_SALTY
AccessioniPrimary (citable) accession number: Q8ZM86
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: March 1, 2002
Last modified: March 28, 2018
This is version 80 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health