PYRF_PYRHO
ID PYRF_PYRHO Reviewed; 208 AA.
AC O58462;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2002, sequence version 2.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Orotidine 5'-phosphate decarboxylase;
DE EC=4.1.1.23;
DE AltName: Full=OMP decarboxylase;
DE Short=OMPDCase;
DE Short=OMPdecase;
GN Name=pyrF; OrderedLocusNames=PH0731;
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 (1.6 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEXES WITH
RP UMP AND XMP, AND SUBUNIT.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RG RIKEN structural genomics initiative (RSGI);
RT "Crystal structure of orotidine 5'-phosphate decarboxylase from Pyrococcus
RT horikoshii OT3.";
RL Submitted (JAN-2006) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the decarboxylation of orotidine 5'-monophosphate
CC (OMP) to uridine 5'-monophosphate (UMP). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + orotidine 5'-phosphate = CO2 + UMP;
CC Xref=Rhea:RHEA:11596, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57538, ChEBI:CHEBI:57865; EC=4.1.1.23;
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC UMP from orotate: step 2/2.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|Ref.2}.
CC -!- SIMILARITY: Belongs to the OMP decarboxylase family. Type 1 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA29822.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; BA000001; BAA29822.1; ALT_INIT; Genomic_DNA.
DR PIR; D71120; D71120.
DR RefSeq; WP_048053207.1; NC_000961.1.
DR PDB; 2CZ5; X-ray; 1.85 A; A/B=1-208.
DR PDB; 2CZD; X-ray; 1.60 A; A/B=1-208.
DR PDB; 2CZE; X-ray; 1.85 A; A/B=1-208.
DR PDB; 2CZF; X-ray; 1.85 A; A/B=1-208.
DR PDBsum; 2CZ5; -.
DR PDBsum; 2CZD; -.
DR PDBsum; 2CZE; -.
DR PDBsum; 2CZF; -.
DR AlphaFoldDB; O58462; -.
DR SMR; O58462; -.
DR STRING; 70601.3257139; -.
DR EnsemblBacteria; BAA29822; BAA29822; BAA29822.
DR GeneID; 1443064; -.
DR KEGG; pho:PH0731; -.
DR eggNOG; arCOG00081; Archaea.
DR OMA; EMSHPGA; -.
DR OrthoDB; 54384at2157; -.
DR UniPathway; UPA00070; UER00120.
DR EvolutionaryTrace; O58462; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0004590; F:orotidine-5'-phosphate decarboxylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IEA:InterPro.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01200_A; OMPdecase_type1_A; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR014732; OMPdecase.
DR InterPro; IPR018089; OMPdecase_AS.
DR InterPro; IPR001754; OMPdeCOase_dom.
DR InterPro; IPR011060; RibuloseP-bd_barrel.
DR PANTHER; PTHR32119:SF2; PTHR32119:SF2; 1.
DR Pfam; PF00215; OMPdecase; 1.
DR SMART; SM00934; OMPdecase; 1.
DR SUPFAM; SSF51366; SSF51366; 1.
DR TIGRFAMs; TIGR01740; pyrF; 1.
DR PROSITE; PS00156; OMPDECASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Lyase; Pyrimidine biosynthesis.
FT CHAIN 1..208
FT /note="Orotidine 5'-phosphate decarboxylase"
FT /id="PRO_0000134616"
FT ACT_SITE 59
FT /note="Proton donor"
FT BINDING 7
FT /ligand="substrate"
FT BINDING 29
FT /ligand="substrate"
FT BINDING 57..66
FT /ligand="substrate"
FT BINDING 109
FT /ligand="substrate"
FT BINDING 162..172
FT /ligand="substrate"
FT BINDING 185
FT /ligand="substrate"
FT BINDING 186
FT /ligand="substrate"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 11..21
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:2CZD"
FT STRAND 26..31
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 32..38
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 42..50
FT /evidence="ECO:0007829|PDB:2CZD"
FT STRAND 53..60
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 64..76
FT /evidence="ECO:0007829|PDB:2CZD"
FT STRAND 80..86
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 90..97
FT /evidence="ECO:0007829|PDB:2CZD"
FT STRAND 100..105
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 111..114
FT /evidence="ECO:0007829|PDB:2CZD"
FT TURN 115..117
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 118..120
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 121..131
FT /evidence="ECO:0007829|PDB:2CZD"
FT STRAND 134..137
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 144..152
FT /evidence="ECO:0007829|PDB:2CZD"
FT STRAND 158..161
FT /evidence="ECO:0007829|PDB:2CZD"
FT STRAND 166..169
FT /evidence="ECO:0007829|PDB:2CZ5"
FT HELIX 170..177
FT /evidence="ECO:0007829|PDB:2CZD"
FT STRAND 180..184
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 186..189
FT /evidence="ECO:0007829|PDB:2CZD"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:2CZD"
FT HELIX 194..205
FT /evidence="ECO:0007829|PDB:2CZD"
SQ SEQUENCE 208 AA; 22692 MW; F0D3124758EB4C43 CRC64;
MIVLALDVYE GERAIKIAKS VKDYISMIKV NWPLILGSGV DIIRRLKEET GVEIIADLKL
ADIPNTNRLI ARKVFGAGAD YVIVHTFVGR DSVMAVKELG EIIMVVEMSH PGALEFINPL
TDRFIEVANE IEPFGVIAPG TRPERIGYIR DRLKEGIKIL APGIGAQGGK AKDAVKAGAD
YIIVGRAIYN APNPREAAKA IYDEIRGV
