IXTPA_PYRHO
ID IXTPA_PYRHO Reviewed; 186 AA.
AC O59580;
DT 28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=dITP/XTP pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_01405};
DE EC=3.6.1.66 {ECO:0000255|HAMAP-Rule:MF_01405};
DE AltName: Full=Non-canonical purine NTP pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_01405};
DE AltName: Full=Non-standard purine NTP pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_01405};
DE AltName: Full=Nucleoside-triphosphate diphosphatase {ECO:0000255|HAMAP-Rule:MF_01405};
DE AltName: Full=Nucleoside-triphosphate pyrophosphatase {ECO:0000255|HAMAP-Rule:MF_01405};
DE Short=NTPase {ECO:0000255|HAMAP-Rule:MF_01405};
GN OrderedLocusNames=PH1917;
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 X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH ITP.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RG RIKEN structural genomics initiative (RSGI);
RT "Structure of nucleotide triphosphate pyrophosphatase from Pyrococcus
RT horikoshii OT3.";
RL Submitted (DEC-2006) to the PDB data bank.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP ITP; IMP AND MN(2+), FUNCTION, COFACTOR, AND SUBUNIT.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=18062990; DOI=10.1016/j.jmb.2007.11.018;
RA Lokanath N.K., Pampa K.J., Takio K., Kunishima N.;
RT "Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase
RT from Pyrococcus horikoshii OT3: functional significance of interprotomer
RT conformational changes.";
RL J. Mol. Biol. 375:1013-1025(2008).
CC -!- FUNCTION: Pyrophosphatase that catalyzes the hydrolysis of nucleoside
CC triphosphates to their monophosphate derivatives, with a high
CC preference for the non-canonical purine nucleotides XTP (xanthosine
CC triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to
CC function as a house-cleaning enzyme that removes non-canonical purine
CC nucleotides from the nucleotide pool, thus preventing their
CC incorporation into DNA/RNA and avoiding chromosomal lesions.
CC {ECO:0000255|HAMAP-Rule:MF_01405, ECO:0000305|PubMed:18062990}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + XTP = diphosphate + H(+) + XMP; Xref=Rhea:RHEA:28610,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:57464, ChEBI:CHEBI:61314; EC=3.6.1.66;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dITP + H2O = dIMP + diphosphate + H(+); Xref=Rhea:RHEA:28342,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:61194, ChEBI:CHEBI:61382; EC=3.6.1.66;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01405};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + ITP = diphosphate + H(+) + IMP; Xref=Rhea:RHEA:29399,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:58053, ChEBI:CHEBI:61402; EC=3.6.1.66;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01405};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01405,
CC ECO:0000305|PubMed:18062990};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000305|PubMed:18062990};
CC Note=Binds 1 divalent metal cation per subunit; can use either Mg(2+)
CC or Mn(2+). {ECO:0000305|PubMed:18062990};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18062990, ECO:0000269|Ref.2}.
CC -!- SIMILARITY: Belongs to the HAM1 NTPase family. {ECO:0000255|HAMAP-
CC Rule:MF_01405}.
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DR EMBL; BA000001; BAA31042.1; -; Genomic_DNA.
DR PIR; C71206; C71206.
DR RefSeq; WP_010885982.1; NC_000961.1.
DR PDB; 1V7R; X-ray; 1.40 A; A=1-186.
DR PDB; 2DVN; X-ray; 1.60 A; A/B=1-186.
DR PDB; 2DVO; X-ray; 2.21 A; A=1-186.
DR PDB; 2DVP; X-ray; 1.90 A; A=1-186.
DR PDB; 2E5X; X-ray; 2.00 A; A=1-186.
DR PDB; 2ZTI; X-ray; 2.60 A; A=1-186.
DR PDBsum; 1V7R; -.
DR PDBsum; 2DVN; -.
DR PDBsum; 2DVO; -.
DR PDBsum; 2DVP; -.
DR PDBsum; 2E5X; -.
DR PDBsum; 2ZTI; -.
DR AlphaFoldDB; O59580; -.
DR SMR; O59580; -.
DR STRING; 70601.3258359; -.
DR EnsemblBacteria; BAA31042; BAA31042; BAA31042.
DR GeneID; 1442764; -.
DR KEGG; pho:PH1917; -.
DR eggNOG; arCOG04184; Archaea.
DR OMA; DCFADDT; -.
DR OrthoDB; 94889at2157; -.
DR BRENDA; 3.6.1.66; 5244.
DR EvolutionaryTrace; O59580; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0035870; F:dITP diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0036220; F:ITP diphosphatase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0017111; F:nucleoside-triphosphatase activity; IEA:InterPro.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0036222; F:XTP diphosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0009117; P:nucleotide metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0009146; P:purine nucleoside triphosphate catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd00515; HAM1; 1.
DR Gene3D; 3.90.950.10; -; 1.
DR HAMAP; MF_01405; Non_canon_purine_NTPase; 1.
DR InterPro; IPR020922; dITP/XTP_pyrophosphatase.
DR InterPro; IPR002637; Ham1p-like.
DR InterPro; IPR029001; ITPase-like_fam.
DR PANTHER; PTHR11067; PTHR11067; 1.
DR Pfam; PF01725; Ham1p_like; 1.
DR SUPFAM; SSF52972; SSF52972; 1.
DR TIGRFAMs; TIGR00042; TIGR00042; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Manganese; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding.
FT CHAIN 1..186
FT /note="dITP/XTP pyrophosphatase"
FT /id="PRO_0000410428"
FT ACT_SITE 65
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01405"
FT BINDING 7..12
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18062990, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2DVO, ECO:0007744|PDB:2E5X"
FT BINDING 36
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305|PubMed:18062990,
FT ECO:0007744|PDB:2ZTI"
FT BINDING 65
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305|PubMed:18062990,
FT ECO:0007744|PDB:2ZTI"
FT BINDING 66
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18062990, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2DVO, ECO:0007744|PDB:2E5X"
FT BINDING 140..143
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18062990, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2DVO, ECO:0007744|PDB:2E5X"
FT BINDING 163
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18062990, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2DVO, ECO:0007744|PDB:2E5X"
FT BINDING 168..169
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18062990, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2DVO, ECO:0007744|PDB:2E5X"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 10..21
FT /evidence="ECO:0007829|PDB:1V7R"
FT TURN 22..24
FT /evidence="ECO:0007829|PDB:1V7R"
FT STRAND 26..30
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 42..53
FT /evidence="ECO:0007829|PDB:1V7R"
FT TURN 54..56
FT /evidence="ECO:0007829|PDB:1V7R"
FT STRAND 59..70
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 71..73
FT /evidence="ECO:0007829|PDB:1V7R"
FT TURN 74..76
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 78..80
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 81..87
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 89..96
FT /evidence="ECO:0007829|PDB:1V7R"
FT TURN 97..99
FT /evidence="ECO:0007829|PDB:1V7R"
FT STRAND 104..115
FT /evidence="ECO:0007829|PDB:1V7R"
FT STRAND 118..130
FT /evidence="ECO:0007829|PDB:1V7R"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:1V7R"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 155..157
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 160..164
FT /evidence="ECO:0007829|PDB:1V7R"
FT HELIX 168..184
FT /evidence="ECO:0007829|PDB:1V7R"
SQ SEQUENCE 186 AA; 21205 MW; 64FD0922B5C74450 CRC64;
MKIFFITSNP GKVREVANFL GTFGIEIVQL KHEYPEIQAE KLEDVVDFGI SWLKGKVPEP
FMIEDSGLFI ESLKGFPGVY SSYVYRTIGL EGILKLMEGA EDRRAYFKSV IGFYIDGKAY
KFSGVTWGRI SNEKRGTHGF GYDPIFIPEG SEKTFAEMTI EEKNALSHRG KALKAFFEWL
KVNLKY
