PYRDB_PYRAB
ID PYRDB_PYRAB Reviewed; 299 AA.
AC Q9V0Y6; G8ZJB1;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2012, sequence version 2.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit;
DE Short=DHOD B;
DE Short=DHODase B;
DE Short=DHOdehase B;
DE EC=1.3.1.14;
DE AltName: Full=Dihydroorotate oxidase B;
DE AltName: Full=Orotate reductase (NADH);
GN Name=pyrD; OrderedLocusNames=PYRAB06530; ORFNames=PAB1936;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC NAD(+) as electron acceptor. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-dihydroorotate + NAD(+) = H(+) + NADH + orotate;
CC Xref=Rhea:RHEA:13513, ChEBI:CHEBI:15378, ChEBI:CHEBI:30839,
CC ChEBI:CHEBI:30864, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.3.1.14;
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210; Evidence={ECO:0000250};
CC Note=Binds 1 FMN per subunit. {ECO:0000250};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC orotate from (S)-dihydroorotate (NAD(+) route): step 1/1.
CC -!- SUBUNIT: Heterotetramer of 2 PyrK and 2 PyrD type B subunits.
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the dihydroorotate dehydrogenase family. Type 1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB49566.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AJ248285; CAB49566.1; ALT_INIT; Genomic_DNA.
DR EMBL; HE613800; CCE70038.1; -; Genomic_DNA.
DR PIR; E75106; E75106.
DR RefSeq; WP_048146595.1; NC_000868.1.
DR AlphaFoldDB; Q9V0Y6; -.
DR SMR; Q9V0Y6; -.
DR STRING; 272844.PAB1936; -.
DR PRIDE; Q9V0Y6; -.
DR EnsemblBacteria; CAB49566; CAB49566; PAB1936.
DR GeneID; 1495551; -.
DR KEGG; pab:PAB1936; -.
DR PATRIC; fig|272844.11.peg.684; -.
DR eggNOG; arCOG00603; Archaea.
DR HOGENOM; CLU_042042_0_1_2; -.
DR OrthoDB; 31316at2157; -.
DR UniPathway; UPA00070; UER00945.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004152; F:dihydroorotate dehydrogenase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004589; F:orotate reductase (NADH) activity; IEA:UniProtKB-EC.
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 CDD; cd04740; DHOD_1B_like; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00224; DHO_dh_type1; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR033888; DHOD_1B.
DR InterPro; IPR005720; Dihydroorotate_DH.
DR InterPro; IPR024920; Dihydroorotate_DH_1.
DR InterPro; IPR012135; Dihydroorotate_DH_1_2.
DR InterPro; IPR001295; Dihydroorotate_DH_CS.
DR Pfam; PF01180; DHO_dh; 1.
DR PIRSF; PIRSF000164; DHO_oxidase; 1.
DR TIGRFAMs; TIGR01037; pyrD_sub1_fam; 1.
DR PROSITE; PS00911; DHODEHASE_1; 1.
DR PROSITE; PS00912; DHODEHASE_2; 1.
PE 3: Inferred from homology;
KW Cytoplasm; Flavoprotein; FMN; NAD; Oxidoreductase; Pyrimidine biosynthesis.
FT CHAIN 1..299
FT /note="Dihydroorotate dehydrogenase B (NAD(+)), catalytic
FT subunit"
FT /id="PRO_0000148412"
FT ACT_SITE 124
FT /note="Nucleophile"
FT BINDING 19
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 43..44
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 43
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 67..71
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 121
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 121
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 159
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 185
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 186..187
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 211
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 237..238
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 259..260
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
SQ SEQUENCE 299 AA; 32175 MW; 639E67B05F8FF333 CRC64;
MLEVNLFGIK FKNPLILASG VVDMTPELLR RAHREGAGGV VTKSIGMEPR KGYENPTIVE
LPYGLINAMG LPNPGWEAFL EEFRKEKFDF PVIVSIFGGT PEEFAFLAEK LGEVADAFEL
NLSCPHAKGY GMEIGQKPEN VYEVVKAVKD VTDKPVIAKL TPNVSDIREL GLAAEKAGAD
GVSAINTVKA IAIDIYAKRP ILSNKFGGYS GPGVKPIALR AVYDLASSLD IPVIGIGGIT
TWQDAVEFLL AGASALQIGT AVYLRGFSVF REIAEGISRY LKEEGYSSVK EIIGLALKV
