VAPC5_MYCTU
ID VAPC5_MYCTU Reviewed; 135 AA.
AC P96917; L0T741;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 2.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Ribonuclease VapC5 {ECO:0000255|HAMAP-Rule:MF_00265};
DE Short=RNase VapC5 {ECO:0000255|HAMAP-Rule:MF_00265};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_00265};
DE AltName: Full=Toxin VapC5 {ECO:0000255|HAMAP-Rule:MF_00265};
GN Name=vapC5 {ECO:0000255|HAMAP-Rule:MF_00265}; OrderedLocusNames=Rv0627;
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 IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
RX PubMed=19099550; DOI=10.1186/1752-0509-2-109;
RA Raman K., Yeturu K., Chandra N.;
RT "targetTB: a target identification pipeline for Mycobacterium tuberculosis
RT through an interactome, reactome and genome-scale structural analysis.";
RL BMC Syst. Biol. 2:109-109(2008).
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 IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION.
RC STRAIN=ATCC 27294 / TMC 102 / H37Rv;
RX PubMed=23345537; DOI=10.1074/mcp.m112.018846;
RA Albrethsen J., Agner J., Piersma S.R., Hoejrup P., Pham T.V., Weldingh K.,
RA Jimenez C.R., Andersen P., Rosenkrands I.;
RT "Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-
RT starvation-responsive toxin-antitoxin systems.";
RL Mol. Cell. Proteomics 12:1180-1191(2013).
RN [6]
RP FUNCTION.
RC STRAIN=H37Rv;
RX PubMed=25622615; DOI=10.1128/jb.02508-14;
RA Jin G., Pavelka M.S. Jr., Butler J.S.;
RT "Structure-function analysis of VapB4 antitoxin identifies critical
RT features of a minimal VapC4 toxin-binding module.";
RL J. Bacteriol. 197:1197-1207(2015).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.76 ANGSTROMS) OF 2-135 IN COMPLEX WITH VAPB5,
RP FUNCTION AS AN RNASE, SUBUNIT, AND COFACTOR.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=18952600; DOI=10.1074/jbc.m805061200;
RA Miallau L., Faller M., Chiang J., Arbing M., Guo F., Cascio D.,
RA Eisenberg D.;
RT "Structure and proposed activity of a member of the VapBC family of toxin-
RT antitoxin systems. VapBC-5 from Mycobacterium tuberculosis.";
RL J. Biol. Chem. 284:276-283(2009).
CC -!- FUNCTION: Probable toxic component of a type II toxin-antitoxin (TA)
CC system. The cognate antitoxin is VapB5. Has limited RNase activity on
CC substrates; activity is seen with a VapC5-VapB5 complex.
CC {ECO:0000269|PubMed:18952600}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00265,
CC ECO:0000269|PubMed:18952600};
CC -!- SUBUNIT: Forms a complex with VapB5. {ECO:0000269|PubMed:18952600}.
CC -!- SUBCELLULAR LOCATION: Secreted. Note=Following 6 weeks of nutrient
CC starvation. {ECO:0000269|PubMed:23345537}.
CC -!- MISCELLANEOUS: Was identified as a high-confidence drug target.
CC -!- SIMILARITY: Belongs to the PINc/VapC protein family.
CC {ECO:0000255|HAMAP-Rule:MF_00265}.
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DR EMBL; AL123456; CCP43368.1; -; Genomic_DNA.
DR PIR; H70611; H70611.
DR RefSeq; NP_215141.1; NC_000962.3.
DR RefSeq; WP_003403246.1; NZ_NVQJ01000033.1.
DR PDB; 3DBO; X-ray; 1.76 A; B=2-135.
DR PDBsum; 3DBO; -.
DR AlphaFoldDB; P96917; -.
DR SMR; P96917; -.
DR STRING; 83332.Rv0627; -.
DR PaxDb; P96917; -.
DR DNASU; 887991; -.
DR GeneID; 887991; -.
DR KEGG; mtu:Rv0627; -.
DR TubercuList; Rv0627; -.
DR eggNOG; COG1487; Bacteria.
DR InParanoid; P96917; -.
DR OMA; YNDLWIA; -.
DR PhylomeDB; P96917; -.
DR EvolutionaryTrace; P96917; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0004521; F:endoribonuclease activity; IDA:MTBBASE.
DR GO; GO:0000287; F:magnesium ion binding; IDA: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; Secreted; Toxin-antitoxin system.
FT CHAIN 1..135
FT /note="Ribonuclease VapC5"
FT /id="PRO_0000407868"
FT DOMAIN 9..130
FT /note="PINc"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT BINDING 11
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT BINDING 100
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT STRAND 7..10
FT /evidence="ECO:0007829|PDB:3DBO"
FT HELIX 13..15
FT /evidence="ECO:0007829|PDB:3DBO"
FT HELIX 26..28
FT /evidence="ECO:0007829|PDB:3DBO"
FT STRAND 31..36
FT /evidence="ECO:0007829|PDB:3DBO"
FT HELIX 37..49
FT /evidence="ECO:0007829|PDB:3DBO"
FT HELIX 53..64
FT /evidence="ECO:0007829|PDB:3DBO"
FT TURN 65..68
FT /evidence="ECO:0007829|PDB:3DBO"
FT HELIX 76..92
FT /evidence="ECO:0007829|PDB:3DBO"
FT HELIX 98..109
FT /evidence="ECO:0007829|PDB:3DBO"
FT STRAND 114..120
FT /evidence="ECO:0007829|PDB:3DBO"
FT HELIX 121..124
FT /evidence="ECO:0007829|PDB:3DBO"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:3DBO"
SQ SEQUENCE 135 AA; 14408 MW; E0763876C27DF722 CRC64;
MSTTPAAGVL DTSVFIATES GRQLDEALIP DRVATTVVTL AELRVGVLAA ATTDIRAQRL
ATLESVADME TLPVDDDAAR MWARLRIHLA ESGRRVRIND LWIAAVAASR ALPVITQDDD
FAALDGAASV EIIRV
