VAPC_SHIFL
ID VAPC_SHIFL Reviewed; 132 AA.
AC O06662; Q7BCI3;
DT 28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 125.
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; Synonyms=mvpA, stborf2; OrderedLocusNames=CP0245;
OS Shigella flexneri.
OG Plasmid pCP301, Plasmid pMYSH6000, and Plasmid pWR100.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Shigella.
OX NCBI_TaxID=623;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=YSH6000 / Serotype 2a; PLASMID=pMYSH6000;
RX PubMed=9171415; DOI=10.1128/jb.179.11.3670-3675.1997;
RA Radnedge L., Davis M.A., Youngren B., Austin S.J.;
RT "Plasmid maintenance functions of the large virulence plasmid of Shigella
RT flexneri.";
RL J. Bacteriol. 179:3670-3675(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=M90T / Serotype 5a; PLASMID=pWR100;
RX PubMed=11115111; DOI=10.1046/j.1365-2958.2000.02179.x;
RA Buchrieser C., Glaser P., Rusniok C., Nedjari H., d'Hauteville H.,
RA Kunst F., Sansonetti P.J., Parsot C.;
RT "The virulence plasmid pWR100 and the repertoire of proteins secreted by
RT the type III secretion apparatus of Shigella flexneri.";
RL Mol. Microbiol. 38:760-771(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=301 / Serotype 2a; PLASMID=pCP301;
RX PubMed=12384590; DOI=10.1093/nar/gkf566;
RA Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J.,
RA Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L.,
RA Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H.,
RA Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.;
RT "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT through comparison with genomes of Escherichia coli K12 and O157.";
RL Nucleic Acids Res. 30:4432-4441(2002).
RN [4]
RP FUNCTION AS A TOXIN, AND EXPRESSION IN E.COLI.
RC STRAIN=YSH6000 / Serotype 2a; PLASMID=pMYSH6000;
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 [5]
RP FUNCTION AS A TOXIN, FUNCTION AS A TRNA ENDONUCLEASE, SUBSTRATE
RP SPECIFICITY, ACTIVITY REGULATION, SUBUNIT, AND INDUCTION.
RC STRAIN=YSH6000 / Serotype 2a; PLASMID=pMYSH6000;
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).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS), INTERACTION WITH VAPB, AND SUBUNIT.
RC STRAIN=YSH6000 / Serotype 2a; PLASMID=pMYSH6000;
RX PubMed=22037005; DOI=10.1016/j.jmb.2011.10.024;
RA Dienemann C., Boggild A., Winther K.S., Gerdes K., Brodersen D.E.;
RT "Crystal structure of the VapBC toxin-antitoxin complex from Shigella
RT flexneri reveals a hetero-octameric DNA-binding assembly.";
RL J. Mol. Biol. 414:713-722(2011).
CC -!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) system. A
CC tRNA-(fMet) endonuclease, it cleaves both charged and uncharged tRNA-
CC (fMet) between positions 38 and 39 at the anticodon stem-loop boundary.
CC Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His), tRNA(Leu), tRNA(Phe)
CC tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression in E.coli inhibits
CC translation, leads to loss of cell growth and degradation of
CC tRNA(fMet); these effects are neutralized by expression of cognate
CC antitoxin VapB. The VapB/VapC complex probably regulates transcription
CC of its own promoter.
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 -!- ACTIVITY REGULATION: Inhibited by EDTA. {ECO:0000269|PubMed:21502523}.
CC -!- SUBUNIT: Forms a hetero-octamer (4 VapB and 4 VapC) complex with
CC antitoxin VapB. The complex binds 2 different sites in the vapBC
CC promoter, probably via VapB dimerization. {ECO:0000269|PubMed:21502523,
CC ECO:0000269|PubMed:22037005}.
CC -!- INDUCTION: Degradation of tRNA(fMet) is induced by chloramphenicol
CC treatment, suggesting the antitoxin is unstable.
CC {ECO:0000269|PubMed:21502523}.
CC -!- SIMILARITY: Belongs to the PINc/VapC protein family. {ECO:0000305}.
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DR EMBL; U82621; AAB58157.1; -; Genomic_DNA.
DR EMBL; AL391753; CAC05862.1; -; Genomic_DNA.
DR EMBL; AF386526; AAL72335.1; -; Genomic_DNA.
DR RefSeq; NP_085412.1; NC_002698.1.
DR RefSeq; NP_858378.1; NC_004851.1.
DR RefSeq; WP_000911311.1; NZ_WPGW01000138.1.
DR RefSeq; YP_009062544.1; NC_024996.1.
DR PDB; 3TND; X-ray; 2.70 A; A/C/E/G=1-132.
DR PDB; 5ECD; X-ray; 1.75 A; A/B=2-132.
DR PDB; 5ECW; X-ray; 1.94 A; A/B=2-132.
DR PDB; 5ECY; X-ray; 2.00 A; A/B/C/D/E/F/G/H=2-132.
DR PDB; 5ED0; X-ray; 2.10 A; A/B/C/D/E/F/G/H/I/J/K/L=2-132.
DR PDBsum; 3TND; -.
DR PDBsum; 5ECD; -.
DR PDBsum; 5ECW; -.
DR PDBsum; 5ECY; -.
DR PDBsum; 5ED0; -.
DR AlphaFoldDB; O06662; -.
DR SMR; O06662; -.
DR STRING; 198214.CP0245; -.
DR PRIDE; O06662; -.
DR EnsemblBacteria; AAL72335; AAL72335; SF_p0245.
DR GeneID; 1238038; -.
DR KEGG; sfl:CP0245; -.
DR PATRIC; fig|198214.7.peg.5506; -.
DR HOGENOM; CLU_118482_5_3_6; -.
DR OMA; NTAEFTR; -.
DR EvolutionaryTrace; O06662; -.
DR Proteomes; UP000001006; Plasmid pCP301.
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 Plasmid; Reference proteome; Toxin-antitoxin system.
FT CHAIN 1..132
FT /note="tRNA(fMet)-specific endonuclease VapC"
FT /id="PRO_0000410981"
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 STRAND 4..6
FT /evidence="ECO:0007829|PDB:5ECD"
FT HELIX 8..16
FT /evidence="ECO:0007829|PDB:5ECD"
FT HELIX 20..28
FT /evidence="ECO:0007829|PDB:5ECD"
FT TURN 29..31
FT /evidence="ECO:0007829|PDB:5ECD"
FT STRAND 32..36
FT /evidence="ECO:0007829|PDB:5ECD"
FT HELIX 37..49
FT /evidence="ECO:0007829|PDB:5ECD"
FT HELIX 53..64
FT /evidence="ECO:0007829|PDB:5ECD"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:5ECD"
FT HELIX 74..90
FT /evidence="ECO:0007829|PDB:5ECD"
FT HELIX 96..107
FT /evidence="ECO:0007829|PDB:5ECD"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:5ECD"
FT HELIX 117..120
FT /evidence="ECO:0007829|PDB:5ECD"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:3TND"
SQ SEQUENCE 132 AA; 14817 MW; 4C64DB25249C2B70 CRC64;
MLKFMLDTNI CIFTIKNKPA SVRERFNLNQ GKMCISSVTL MELIYGAEKS QMPERNLAVI
EGFVSRIDVL DYDAAAATHT GQIRAELARQ GRPVGPFDQM IAGHARSRGL IIVTNNTREF
ERVGGLRTED WS
