Q8ZM86 (VAPC_SALTY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA(fMet)-specific endonuclease VapC
EC=3.1.-.-

Alternative name(s):
RNase VapC
Toxin VapC

Gene names

Name:	vapC
Ordered Locus Names:	STM3033

Organism

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) [Reference proteome] [HAMAP]

Taxonomic identifier

99287 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella › Salmonella choleraesuis › Salmonella enterica I › Salmonella typhimurium

Protein attributes

Sequence length	132 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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). Ref.2 Ref.3 Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity. Ref.2 Ref.3
Cofactor	Magnesium Potential.
Subunit structure	Forms a complex with antitoxin VapB Probable.
Induction	Induced by amino acid starvation and by chloramphenicol treatment. Ref.2
Sequence similarities	Belongs to the PINc/VapC protein family. Contains 1 PINc domain.

Ontologies

Keywords
Ligand	Magnesium Metal-binding
Molecular function	Endonuclease Hydrolase Nuclease Toxin
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
Molecular_function	endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: HAMAP ribonuclease activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 132	132	tRNA(fMet)-specific endonuclease VapC HAMAP-Rule MF_00265		PRO_0000410980
Regions
	Domain	5 – 131	127	PINc
Sites
	Metal binding	7	1	Magnesium Potential
	Metal binding	98	1	Magnesium Potential
Experimental info
	Mutagenesis	7	1	D → A: No inhibition of cell growth, no degradation of tRNA(fMet). Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Q8ZM86 [UniParc]. Last modified March 1, 2002. Version 1. Checksum: 4AA4120DAD6B6057	FASTA	132	14,938
	10 20 30 40 50 60 MLKFMLDTNT CIFTIKNKPE HIRERFNLNT SRMCISSITL MELIYGAEKS LAPERNLAVV 70 80 90 100 110 120 EGFISRLEVL DYDTQAAIHT GQIRAELARK GTPVGPYDQM IAGHAGSRGL VVVTNNLREF 130 ERIPGIRIED WC

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2." McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K. Nature 413:852-856(2001) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE006468 Genomic DNA. Translation: AAL21909.1.
RefSeq	NP_461950.1. NC_003197.1.
3D structure databases
ProteinModelPortal	Q8ZM86.
ModBase	Search...
Protein-protein interaction databases
STRING	99287.STM3033.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAL21909; AAL21909; STM3033.
GeneID	1254556.
KEGG	stm:STM3033.
PATRIC	32384803. VBISalEnt20916_3211.
Phylogenomic databases
HOGENOM	HOG000121274.
KO	K07062.
OMA	KAELFYG.
ProtClustDB	PRK13725.
Enzyme and pathway databases
BioCyc	SENT99287:GCTI-3053-MONOMER.
Family and domain databases
HAMAP	MF_00265. VapC.
InterPro	IPR002716. PIN_dom. IPR006596. PINc_nuc-bd. IPR022907. VapC_family. [Graphical view]
Pfam	PF01850. PIN. 1 hit. [Graphical view]
SMART	SM00670. PINc. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

VAPC_SALTY

Accession

Primary (citable) accession number: Q8ZM86

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 28, 2011
Last sequence update:	March 1, 2002
Last modified:	May 29, 2013
This is version 51 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program