VAPC_SALTY
ID VAPC_SALTY Reviewed; 132 AA.
AC Q8ZM86;
DT 28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 96.
DE RecName: Full=tRNA(fMet)-specific endonuclease VapC;
DE EC=3.1.-.-;
DE AltName: Full=RNase VapC;
DE AltName: Full=Toxin VapC;
GN Name=vapC; OrderedLocusNames=STM3033;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP FUNCTION AS A TOXIN, INDUCTION, AND EXPRESSION IN E.COLI.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=19400780; DOI=10.1111/j.1365-2958.2009.06694.x;
RA Winther K.S., Gerdes K.;
RT "Ectopic production of VapCs from Enterobacteria inhibits translation and
RT trans-activates YoeB mRNA interferase.";
RL Mol. Microbiol. 72:918-930(2009).
RN [3]
RP FUNCTION AS A TOXIN, FUNCTION AS A TRNA ENDONUCLEASE, SUBSTRATE
RP SPECIFICITY, AND MUTAGENESIS OF ASP-7.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=21502523; DOI=10.1073/pnas.1019587108;
RA Winther K.S., Gerdes K.;
RT "Enteric virulence associated protein VapC inhibits translation by cleavage
RT of initiator tRNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:7403-7407(2011).
CC -!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) system. A
CC site-specific tRNA-(fMet) endonuclease, it cleaves both charged and
CC uncharged tRNA-(fMet) between positions 38 and 39 at the anticodon
CC stem-loop boundary. Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His),
CC tRNA(Leu), tRNA(Phe) tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression
CC in E.coli inhibits translation, leads to loss of cell growth and
CC degradation of tRNA(fMet), these effects are neutralized by expression
CC of cognate antitoxin VapB. Expression also activates translation
CC initiation at correctly positioned elongator codons (AAA and to a
CC lesser extent AAG).
CC -!- FUNCTION: Ectopic overexpression in E.coli induces the YoeB toxin, but
CC this is not the cause of VapC toxicity.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000305};
CC -!- SUBUNIT: Forms a complex with antitoxin VapB. {ECO:0000305}.
CC -!- INDUCTION: Induced by amino acid starvation and by chloramphenicol
CC treatment. {ECO:0000269|PubMed:19400780}.
CC -!- SIMILARITY: Belongs to the PINc/VapC protein family. {ECO:0000305}.
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DR EMBL; AE006468; AAL21909.1; -; Genomic_DNA.
DR RefSeq; NP_461950.1; NC_003197.2.
DR RefSeq; WP_000911336.1; NC_003197.2.
DR PDB; 6IFC; X-ray; 1.99 A; A/C/E/G=1-132.
DR PDB; 6IFM; X-ray; 2.80 A; A/C/E/G=1-132.
DR PDBsum; 6IFC; -.
DR PDBsum; 6IFM; -.
DR AlphaFoldDB; Q8ZM86; -.
DR SMR; Q8ZM86; -.
DR STRING; 99287.STM3033; -.
DR PaxDb; Q8ZM86; -.
DR EnsemblBacteria; AAL21909; AAL21909; STM3033.
DR GeneID; 1254556; -.
DR KEGG; stm:STM3033; -.
DR PATRIC; fig|99287.12.peg.3211; -.
DR HOGENOM; CLU_118482_5_3_6; -.
DR OMA; PYDLQIA; -.
DR PhylomeDB; Q8ZM86; -.
DR BioCyc; SENT99287:STM3033-MON; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004540; F:ribonuclease activity; IEA:InterPro.
DR HAMAP; MF_00265; VapC_Nob1; 1.
DR InterPro; IPR029060; PIN-like_dom_sf.
DR InterPro; IPR002716; PIN_dom.
DR InterPro; IPR022907; VapC_family.
DR Pfam; PF01850; PIN; 1.
DR SUPFAM; SSF88723; SSF88723; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Endonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Reference proteome; Toxin-antitoxin system.
FT CHAIN 1..132
FT /note="tRNA(fMet)-specific endonuclease VapC"
FT /id="PRO_0000410980"
FT DOMAIN 5..131
FT /note="PINc"
FT BINDING 7
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255"
FT BINDING 98
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255"
FT MUTAGEN 7
FT /note="D->A: No inhibition of cell growth, no degradation
FT of tRNA(fMet)."
FT /evidence="ECO:0000269|PubMed:21502523"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:6IFC"
FT HELIX 8..17
FT /evidence="ECO:0007829|PDB:6IFC"
FT HELIX 20..28
FT /evidence="ECO:0007829|PDB:6IFC"
FT TURN 29..31
FT /evidence="ECO:0007829|PDB:6IFC"
FT STRAND 32..36
FT /evidence="ECO:0007829|PDB:6IFC"
FT HELIX 37..49
FT /evidence="ECO:0007829|PDB:6IFC"
FT STRAND 50..52
FT /evidence="ECO:0007829|PDB:6IFC"
FT HELIX 53..65
FT /evidence="ECO:0007829|PDB:6IFC"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:6IFC"
FT HELIX 74..89
FT /evidence="ECO:0007829|PDB:6IFC"
FT HELIX 96..107
FT /evidence="ECO:0007829|PDB:6IFC"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:6IFC"
FT HELIX 117..120
FT /evidence="ECO:0007829|PDB:6IFC"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:6IFC"
SQ SEQUENCE 132 AA; 14938 MW; 4AA4120DAD6B6057 CRC64;
MLKFMLDTNT CIFTIKNKPE HIRERFNLNT SRMCISSITL MELIYGAEKS LAPERNLAVV
EGFISRLEVL DYDTQAAIHT GQIRAELARK GTPVGPYDQM IAGHAGSRGL VVVTNNLREF
ERIPGIRIED WC
