ID   VAPB_SHIFL              Reviewed;          75 AA.
AC   O06663;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-JUL-1997, sequence version 1.
DT   25-MAY-2022, entry version 100.
DE   RecName: Full=Antitoxin VapB;
GN   Name=vapB; OrderedLocusNames=CP0246;
OS   Shigella flexneri.
OG   Plasmid pMYSH6000, and Plasmid pCP301.
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 [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   [3]
RP   FUNCTION AS AN ANTITOXIN.
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   [4]
RP   FUNCTION AS AN ANTITOXIN, 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   [5]
RP   X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 2-75, INTERACTION WITH VAPC,
RP   SUBUNIT, AND DNA-BINDING.
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: Antitoxin component of a type II toxin-antitoxin (TA) system.
CC       Upon expression in E.coli neutralizes the effect of cognate toxin VapC.
CC       The VapB/VapC complex probably regulates transcription of its own
CC       promoter. {ECO:0000269|PubMed:19400780, ECO:0000269|PubMed:21502523}.
CC   -!- SUBUNIT: Homodimer (Probable). Forms a hetero-octamer (4 VapB and 4
CC       VapC) complex with toxin VapC. The complex binds 2 different sites in
CC       the vapBC promoter, probably via VapB dimerization.
CC       {ECO:0000269|PubMed:21502523, ECO:0000269|PubMed:22037005,
CC       ECO:0000305}.
CC   -!- INDUCTION: Degradation of tRNA(fMet) is induced by chloramphenicol
CC       treatment, suggesting the antitoxin is unstable when the growth rate
CC       decreases. {ECO:0000269|PubMed:21502523}.
CC   -!- SIMILARITY: Belongs to the VapB family. {ECO:0000305}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; U82621; AAB58158.1; -; Genomic_DNA.
DR   EMBL; AF386526; AAL72334.1; -; Genomic_DNA.
DR   RefSeq; NP_858379.1; NC_004851.1.
DR   RefSeq; WP_000450531.1; NZ_WPGW01000138.1.
DR   PDB; 3TND; X-ray; 2.70 A; B/D/F/H=2-75.
DR   PDBsum; 3TND; -.
DR   AlphaFoldDB; O06663; -.
DR   SMR; O06663; -.
DR   STRING; 198214.CP0246; -.
DR   EnsemblBacteria; AAL72334; AAL72334; SF_p0246.
DR   GeneID; 1238037; -.
DR   KEGG; sfl:CP0246; -.
DR   PATRIC; fig|198214.7.peg.5507; -.
DR   HOGENOM; CLU_162018_3_2_6; -.
DR   OMA; VFTNNRS; -.
DR   EvolutionaryTrace; O06663; -.
DR   Proteomes; UP000001006; Plasmid pCP301.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   InterPro; IPR007159; SpoVT-AbrB_dom.
DR   InterPro; IPR037914; SpoVT-AbrB_sf.
DR   Pfam; PF04014; MazE_antitoxin; 1.
DR   SUPFAM; SSF89447; SSF89447; 1.
DR   PROSITE; PS51740; SPOVT_ABRB; 1.
PE   1: Evidence at protein level;
KW   3D-structure; DNA-binding; Plasmid; Reference proteome;
KW   Toxin-antitoxin system.
FT   CHAIN           1..75
FT                   /note="Antitoxin VapB"
FT                   /id="PRO_0000219873"
FT   DOMAIN          3..45
FT                   /note="SpoVT-AbrB"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01076"
FT   STRAND          2..7
FT                   /evidence="ECO:0007829|PDB:3TND"
FT   STRAND          9..16
FT                   /evidence="ECO:0007829|PDB:3TND"
FT   HELIX           18..20
FT                   /evidence="ECO:0007829|PDB:3TND"
FT   STRAND          28..34
FT                   /evidence="ECO:0007829|PDB:3TND"
FT   STRAND          37..42
FT                   /evidence="ECO:0007829|PDB:3TND"
FT   HELIX           48..52
FT                   /evidence="ECO:0007829|PDB:3TND"
FT   TURN            58..61
FT                   /evidence="ECO:0007829|PDB:3TND"
SQ   SEQUENCE   75 AA;  8566 MW;  5CD06064DF765B21 CRC64;
     METTVFLSNR SQAVRLPKAV ALPENVKRVE VIAVGRTRII TPAGETWDEW FDGHSVSTDF
     MDNREQPGMQ ERESF