VAPC4_PYRHO
ID VAPC4_PYRHO Reviewed; 149 AA.
AC O58236;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Ribonuclease VapC4 {ECO:0000255|HAMAP-Rule:MF_00265};
DE Short=RNase VapC4 {ECO:0000255|HAMAP-Rule:MF_00265};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_00265};
DE AltName: Full=Putative toxin VapC4 {ECO:0000255|HAMAP-Rule:MF_00265};
GN Name=vapC4 {ECO:0000255|HAMAP-Rule:MF_00265}; OrderedLocusNames=PH0500;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP POSSIBLE FUNCTION.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
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 X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), AND SUBUNIT.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=16511069; DOI=10.1107/s1744309105012406;
RA Jeyakanthan J., Inagaki E., Kuroishi C., Tahirov T.H.;
RT "Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.";
RL Acta Crystallogr. F 61:463-468(2005).
CC -!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) system. An
CC RNase. {ECO:0000255|HAMAP-Rule:MF_00265}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00265};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16511069}.
CC -!- SIMILARITY: Belongs to the PINc/VapC protein family.
CC {ECO:0000255|HAMAP-Rule:MF_00265}.
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DR EMBL; BA000001; BAA29588.1; -; Genomic_DNA.
DR PIR; G71162; G71162.
DR RefSeq; WP_010884604.1; NC_000961.1.
DR PDB; 1V96; X-ray; 1.75 A; A/B=1-149.
DR PDB; 1YE5; X-ray; 2.00 A; A/B=1-149.
DR PDB; 5H4G; X-ray; 1.77 A; A/B=1-149.
DR PDB; 5H4H; X-ray; 2.23 A; A/B=1-149.
DR PDBsum; 1V96; -.
DR PDBsum; 1YE5; -.
DR PDBsum; 5H4G; -.
DR PDBsum; 5H4H; -.
DR AlphaFoldDB; O58236; -.
DR SMR; O58236; -.
DR EnsemblBacteria; BAA29588; BAA29588; BAA29588.
DR GeneID; 1444391; -.
DR KEGG; pho:PH0500; -.
DR eggNOG; arCOG02224; Archaea.
DR OMA; LMISVEM; -.
DR OrthoDB; 98964at2157; -.
DR EvolutionaryTrace; O58236; -.
DR Proteomes; UP000000752; Chromosome.
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; IPR022907; VapC_family.
DR InterPro; IPR016647; VapV_Thermo.
DR PIRSF; PIRSF016154; NA-bd_PIN_PH0500; 1.
DR SUPFAM; SSF88723; SSF88723; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Toxin-antitoxin system.
FT CHAIN 1..149
FT /note="Ribonuclease VapC4"
FT /id="PRO_0000407906"
FT DOMAIN 8..125
FT /note="PINc"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT BINDING 10
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT BINDING 98
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00265"
FT STRAND 5..9
FT /evidence="ECO:0007829|PDB:1V96"
FT HELIX 11..17
FT /evidence="ECO:0007829|PDB:1V96"
FT HELIX 20..22
FT /evidence="ECO:0007829|PDB:1V96"
FT HELIX 23..32
FT /evidence="ECO:0007829|PDB:1V96"
FT STRAND 34..38
FT /evidence="ECO:0007829|PDB:1V96"
FT HELIX 39..48
FT /evidence="ECO:0007829|PDB:1V96"
FT TURN 49..52
FT /evidence="ECO:0007829|PDB:1YE5"
FT HELIX 56..66
FT /evidence="ECO:0007829|PDB:1V96"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:1V96"
FT HELIX 74..89
FT /evidence="ECO:0007829|PDB:1V96"
FT HELIX 96..108
FT /evidence="ECO:0007829|PDB:1V96"
FT STRAND 111..115
FT /evidence="ECO:0007829|PDB:1V96"
FT HELIX 117..120
FT /evidence="ECO:0007829|PDB:1V96"
FT HELIX 121..126
FT /evidence="ECO:0007829|PDB:1V96"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:1V96"
FT HELIX 133..147
FT /evidence="ECO:0007829|PDB:1V96"
SQ SEQUENCE 149 AA; 17190 MW; 76F2B16106A881E4 CRC64;
MPLPPDITFD SLALIKMHSQ NMKRILEVTL AKFTVNLSIV TVYRYLTARA YLKKNIEAEF
EILKDIYNIV PLLDDIAIKA AQIEANLIKK EITLDMEDII TATTAIYTNS LLVTDDPKRY
EPIRRFGLDT MPLDKFIKEV ELMVEKELI
