VAPC2_MYCTU
ID VAPC2_MYCTU Reviewed; 141 AA.
AC P9WFB9; L0T386; O07228; Q7DA25;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 39.
DE RecName: Full=Ribonuclease VapC2 {ECO:0000255|HAMAP-Rule:MF_00265};
DE Short=RNase VapC2 {ECO:0000255|HAMAP-Rule:MF_00265};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_00265};
DE AltName: Full=Toxin VapC2 {ECO:0000255|HAMAP-Rule:MF_00265};
GN Name=vapC2 {ECO:0000255|HAMAP-Rule:MF_00265}; OrderedLocusNames=Rv0301;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP POSSIBLE FUNCTION.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=15718296; DOI=10.1093/nar/gki201;
RA Pandey D.P., Gerdes K.;
RT "Toxin-antitoxin loci are highly abundant in free-living but lost from
RT host-associated prokaryotes.";
RL Nucleic Acids Res. 33:966-976(2005).
RN [3]
RP EXPRESSION IN M.SMEGMATIS, FUNCTION AS A TOXIN, AND FUNCTION AS AN RNASE.
RC STRAIN=ATCC 35801 / TMC 107 / Erdman;
RX PubMed=20011113; DOI=10.1371/journal.pgen.1000767;
RA Ramage H.R., Connolly L.E., Cox J.S.;
RT "Comprehensive functional analysis of Mycobacterium tuberculosis toxin-
RT antitoxin systems: implications for pathogenesis, stress responses, and
RT evolution.";
RL PLoS Genet. 5:E1000767-E1000767(2009).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.49 ANGSTROMS) OF 2-141 IN COMPLEX WITH MAGNESIUM,
RP AND SUBUNIT.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=23011806; DOI=10.1002/pro.2161;
RA Min A.B., Miallau L., Sawaya M.R., Habel J., Cascio D., Eisenberg D.;
RT "The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex
RT from M. tuberculosis reveals a Mg(2+) ion in the active site and a putative
RT RNA-binding Site.";
RL Protein Sci. 21:1754-1767(2012).
CC -!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) system.
CC Acts as an RNase. Upon expression in M.smegmatis inhibits translation,
CC growth and colony formation. All its toxic effects are neutralized by
CC coexpression with cognate antitoxin VapB2.
CC {ECO:0000269|PubMed:20011113}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 Mg(2+) ion per monomer; in the crystal structure only 1
CC toxin is bound to Mg(2+).;
CC -!- SUBUNIT: Probably active as a homodimer, which binds to a VapB2
CC antitoxin homodimer, which then oligomerizes further to a hetero-
CC octamer. When in complex with antitoxin VapB2 the toxin activity is
CC inhibited; 1 VapB2 may suffice to inhibit toxin.
CC {ECO:0000269|PubMed:23011806}.
CC -!- SIMILARITY: Belongs to the PINc/VapC protein family.
CC {ECO:0000255|HAMAP-Rule:MF_00265}.
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DR EMBL; AL123456; CCP43031.1; -; Genomic_DNA.
DR PIR; F70523; F70523.
DR RefSeq; NP_214815.1; NC_000962.3.
DR RefSeq; WP_003401566.1; NZ_NVQJ01000026.1.
DR PDB; 3H87; X-ray; 1.49 A; A/B=2-141.
DR PDBsum; 3H87; -.
DR AlphaFoldDB; P9WFB9; -.
DR SMR; P9WFB9; -.
DR STRING; 83332.Rv0301; -.
DR PaxDb; P9WFB9; -.
DR GeneID; 886586; -.
DR KEGG; mtu:Rv0301; -.
DR PATRIC; fig|83332.111.peg.337; -.
DR TubercuList; Rv0301; -.
DR eggNOG; COG1487; Bacteria.
DR OMA; YDRDFET; -.
DR PhylomeDB; P9WFB9; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004540; F:ribonuclease activity; IDA:MTBBASE.
DR GO; GO:0017148; P:negative regulation of translation; IMP:MTBBASE.
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; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Reference proteome; Toxin-antitoxin system.
FT CHAIN 1..141
FT /note="Ribonuclease VapC2"
FT /id="PRO_0000407865"
FT DOMAIN 7..129
FT /note="PINc"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT BINDING 99
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265,
FT ECO:0000269|PubMed:23011806"
FT BINDING 117
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265,
FT ECO:0000269|PubMed:23011806"
FT BINDING 119
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265,
FT ECO:0000269|PubMed:23011806"
FT STRAND 6..8
FT /evidence="ECO:0007829|PDB:3H87"
FT HELIX 10..13
FT /evidence="ECO:0007829|PDB:3H87"
FT HELIX 14..18
FT /evidence="ECO:0007829|PDB:3H87"
FT HELIX 22..30
FT /evidence="ECO:0007829|PDB:3H87"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:3H87"
FT HELIX 38..47
FT /evidence="ECO:0007829|PDB:3H87"
FT STRAND 48..50
FT /evidence="ECO:0007829|PDB:3H87"
FT HELIX 51..59
FT /evidence="ECO:0007829|PDB:3H87"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:3H87"
FT HELIX 73..88
FT /evidence="ECO:0007829|PDB:3H87"
FT HELIX 97..109
FT /evidence="ECO:0007829|PDB:3H87"
FT STRAND 112..116
FT /evidence="ECO:0007829|PDB:3H87"
FT HELIX 119..127
FT /evidence="ECO:0007829|PDB:3H87"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:3H87"
SQ SEQUENCE 141 AA; 15746 MW; F371180C7C34F448 CRC64;
MTDQRWLIDK SALVRLTDSP DMEIWSNRIE RGLVHITGVT RLEVGFSAEC GEIARREFRE
PPLSAMPVEY LTPRIEDRAL EVQTLLADRG HHRGPSIPDL LIAATAELSG LTVLHVDKDF
DAIAALTGQK TERLTHRPPS A
