VAPC9_PYRAE
ID VAPC9_PYRAE Reviewed; 133 AA.
AC Q8ZUJ3;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 102.
DE RecName: Full=Exonuclease VapC9;
DE AltName: Full=Putative toxin VapC9 {ECO:0000255|HAMAP-Rule:MF_00265};
DE AltName: Full=Ribonuclease VapC9 {ECO:0000255|HAMAP-Rule:MF_00265};
DE Short=RNase VapC9 {ECO:0000255|HAMAP-Rule:MF_00265};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_00265};
GN Name=vapC9 {ECO:0000255|HAMAP-Rule:MF_00265}; OrderedLocusNames=PAE2754;
OS Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP
OS 104966 / NBRC 100827 / IM2).
OC Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae;
OC Pyrobaculum.
OX NCBI_TaxID=178306;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2;
RX PubMed=11792869; DOI=10.1073/pnas.241636498;
RA Fitz-Gibbon S.T., Ladner H., Kim U.-J., Stetter K.O., Simon M.I.,
RA Miller J.H.;
RT "Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum
RT aerophilum.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:984-989(2002).
RN [2]
RP POSSIBLE FUNCTION.
RC STRAIN=ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2;
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 PRELIMINARY CRYSTALLIZATION, AND MUTAGENESIS OF LEU-65 AND LEU-80.
RC STRAIN=ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2;
RX PubMed=15039569; DOI=10.1107/s0907444904002021;
RA Backbro K., Roos A., Baker E.N., Arcus V.L.;
RT "Crystallization and preliminary X-ray analysis of a conserved hypothetical
RT protein PAE2754 from Pyrobaculum aerophilum and of a double Leu-->Met
RT mutant engineered for MAD phasing.";
RL Acta Crystallogr. D 60:733-735(2004).
RN [4]
RP FUNCTION, ACTIVITY REGULATION, AND COFACTOR.
RX PubMed=22539524; DOI=10.1261/rna.031229.111;
RA McKenzie J.L., Duyvestyn J.M., Smith T., Bendak K., Mackay J., Cursons R.,
RA Cook G.M., Arcus V.L.;
RT "Determination of ribonuclease sequence-specificity using Pentaprobes and
RT mass spectrometry.";
RL RNA 18:1267-1278(2012).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.52 ANGSTROMS) OF 3-133, SUBUNIT, EXONUCLEASE
RP ACTIVITY, AND COFACTOR.
RC STRAIN=ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2;
RX PubMed=14734548; DOI=10.1074/jbc.m313833200;
RA Arcus V.L., Backbro K., Roos A., Daniel E.L., Baker E.N.;
RT "Distant structural homology leads to the functional characterization of an
RT archaeal PIN domain as an exonuclease.";
RL J. Biol. Chem. 279:16471-16478(2004).
CC -!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) system (By
CC similarity). Has ribonuclease activity. Has a slow ssDNA exonuclease
CC activity. {ECO:0000250, ECO:0000269|PubMed:22539524}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00265,
CC ECO:0000269|PubMed:14734548, ECO:0000269|PubMed:22539524};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA. {ECO:0000269|PubMed:22539524}.
CC -!- SUBUNIT: Homodimer, 2 of which then form a homotetramer.
CC {ECO:0000269|PubMed:14734548}.
CC -!- SIMILARITY: Belongs to the PINc/VapC protein family.
CC {ECO:0000255|HAMAP-Rule:MF_00265}.
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DR EMBL; AE009441; AAL64414.1; -; Genomic_DNA.
DR PDB; 1V8O; X-ray; 2.80 A; A/B/C/D/E/F/G/H=1-133.
DR PDB; 1V8P; X-ray; 2.52 A; A/B/C/D/E/F/G/H/I/J/K/L=1-133.
DR PDBsum; 1V8O; -.
DR PDBsum; 1V8P; -.
DR AlphaFoldDB; Q8ZUJ3; -.
DR SMR; Q8ZUJ3; -.
DR STRING; 178306.PAE2754; -.
DR EnsemblBacteria; AAL64414; AAL64414; PAE2754.
DR KEGG; pai:PAE2754; -.
DR PATRIC; fig|178306.9.peg.2054; -.
DR eggNOG; arCOG00729; Archaea.
DR HOGENOM; CLU_121774_5_0_2; -.
DR InParanoid; Q8ZUJ3; -.
DR OMA; GNALWKE; -.
DR EvolutionaryTrace; Q8ZUJ3; -.
DR Proteomes; UP000002439; Chromosome.
DR GO; GO:0004527; F:exonuclease 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 CDD; cd09873; PIN_Pae0151-like; 1.
DR HAMAP; MF_00265; VapC_Nob1; 1.
DR InterPro; IPR029060; PIN-like_dom_sf.
DR InterPro; IPR002716; PIN_dom.
DR InterPro; IPR044153; PIN_Pae0151-like.
DR InterPro; IPR022907; VapC_family.
DR Pfam; PF01850; PIN; 1.
DR SUPFAM; SSF88723; SSF88723; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Reference proteome; Toxin-antitoxin system.
FT CHAIN 1..133
FT /note="Exonuclease VapC9"
FT /id="PRO_0000407904"
FT DOMAIN 5..113
FT /note="PINc"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT BINDING 8
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT BINDING 92
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT BINDING 110
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT MUTAGEN 65
FT /note="L->M: Facilitates structure determination."
FT /evidence="ECO:0000269|PubMed:15039569"
FT MUTAGEN 80
FT /note="L->M: Facilitates structure determination."
FT /evidence="ECO:0000269|PubMed:15039569"
FT STRAND 5..7
FT /evidence="ECO:0007829|PDB:1V8P"
FT HELIX 9..15
FT /evidence="ECO:0007829|PDB:1V8P"
FT HELIX 19..22
FT /evidence="ECO:0007829|PDB:1V8P"
FT HELIX 23..28
FT /evidence="ECO:0007829|PDB:1V8P"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:1V8P"
FT HELIX 33..48
FT /evidence="ECO:0007829|PDB:1V8P"
FT HELIX 54..66
FT /evidence="ECO:0007829|PDB:1V8P"
FT STRAND 68..70
FT /evidence="ECO:0007829|PDB:1V8P"
FT HELIX 76..86
FT /evidence="ECO:0007829|PDB:1V8P"
FT HELIX 90..101
FT /evidence="ECO:0007829|PDB:1V8P"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:1V8P"
FT HELIX 111..116
FT /evidence="ECO:0007829|PDB:1V8P"
FT HELIX 123..132
FT /evidence="ECO:0007829|PDB:1V8P"
SQ SEQUENCE 133 AA; 14909 MW; 0FB860A7C861F776 CRC64;
MPVEYLVDAS ALYALAAHYD KWIKHREKLA ILHLTIYEAG NALWKEARLG RVDWAAASRH
LKKVLSSFKV LEDPPLDEVL RVAVERGLTF YDASYAYVAE SSGLVLVTQD RELLAKTKGA
IDVETLLVRL AAQ
