PYRD_MYCGI
ID PYRD_MYCGI Reviewed; 353 AA.
AC A4TB97;
DT 20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT 15-MAY-2007, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=Dihydroorotate dehydrogenase (quinone) {ECO:0000255|HAMAP-Rule:MF_00225};
DE EC=1.3.5.2 {ECO:0000255|HAMAP-Rule:MF_00225};
DE AltName: Full=DHOdehase {ECO:0000255|HAMAP-Rule:MF_00225};
DE Short=DHOD {ECO:0000255|HAMAP-Rule:MF_00225};
DE Short=DHODase {ECO:0000255|HAMAP-Rule:MF_00225};
DE AltName: Full=Dihydroorotate oxidase {ECO:0000255|HAMAP-Rule:MF_00225};
GN Name=pyrD {ECO:0000255|HAMAP-Rule:MF_00225}; OrderedLocusNames=Mflv_3039;
OS Mycolicibacterium gilvum (strain PYR-GCK) (Mycobacterium gilvum (strain
OS PYR-GCK)).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycolicibacterium.
OX NCBI_TaxID=350054;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PYR-GCK;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Mikhailova N., Miller C., Richardson P.;
RT "Complete sequence of chromosome of Mycobacterium gilvum PYR-GCK.";
RL Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC quinone as electron acceptor. {ECO:0000255|HAMAP-Rule:MF_00225}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-dihydroorotate + a quinone = a quinol + orotate;
CC Xref=Rhea:RHEA:30187, ChEBI:CHEBI:24646, ChEBI:CHEBI:30839,
CC ChEBI:CHEBI:30864, ChEBI:CHEBI:132124; EC=1.3.5.2;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00225};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00225};
CC Note=Binds 1 FMN per subunit. {ECO:0000255|HAMAP-Rule:MF_00225};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC orotate from (S)-dihydroorotate (quinone route): step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_00225}.
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00225}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000255|HAMAP-Rule:MF_00225};
CC Peripheral membrane protein {ECO:0000255|HAMAP-Rule:MF_00225}.
CC -!- SIMILARITY: Belongs to the dihydroorotate dehydrogenase family. Type 2
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_00225}.
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DR EMBL; CP000656; ABP45516.1; -; Genomic_DNA.
DR RefSeq; WP_011893917.1; NC_009338.1.
DR AlphaFoldDB; A4TB97; -.
DR SMR; A4TB97; -.
DR STRING; 350054.Mflv_3039; -.
DR EnsemblBacteria; ABP45516; ABP45516; Mflv_3039.
DR KEGG; mgi:Mflv_3039; -.
DR eggNOG; COG0167; Bacteria.
DR HOGENOM; CLU_013640_2_0_11; -.
DR OMA; ERIKMGA; -.
DR OrthoDB; 1109542at2; -.
DR UniPathway; UPA00070; UER00946.
DR GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0004152; F:dihydroorotate dehydrogenase 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 CDD; cd04738; DHOD_2_like; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00225; DHO_dh_type2; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR005720; Dihydroorotate_DH.
DR InterPro; IPR012135; Dihydroorotate_DH_1_2.
DR InterPro; IPR005719; Dihydroorotate_DH_2.
DR InterPro; IPR001295; Dihydroorotate_DH_CS.
DR Pfam; PF01180; DHO_dh; 1.
DR PIRSF; PIRSF000164; DHO_oxidase; 1.
DR TIGRFAMs; TIGR01036; pyrD_sub2; 1.
DR PROSITE; PS00911; DHODEHASE_1; 1.
DR PROSITE; PS00912; DHODEHASE_2; 1.
PE 3: Inferred from homology;
KW Cell membrane; Flavoprotein; FMN; Membrane; Oxidoreductase;
KW Pyrimidine biosynthesis.
FT CHAIN 1..353
FT /note="Dihydroorotate dehydrogenase (quinone)"
FT /id="PRO_1000078160"
FT ACT_SITE 179
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 66..70
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 70
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 90
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 115..119
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 143
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 176
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 176
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 181
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 212
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 240
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 241..242
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 264
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 293
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
FT BINDING 314..315
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00225"
SQ SEQUENCE 353 AA; 36664 MW; 3235AA5366E72A3C CRC64;
MYGALRKALF LVPPERIHGL VFAGLRAATT PVPLRRSLSR RLAPHDPVLA STVFGVRFPG
PLGLAAGFDK DGLGVHTWGA LGFGYAELGT VTAQAQPGNP PPRMFRLPAD RALLNRMGFN
NHGSAALALQ LARSSSDVPI GVNIGKTKVT EPQDAPADYA ESARLLGSLA AYLVVNVSSP
NTPGLRDLQS VESLRPILSA VLAETSTPVL VKIAPDLADT DIDDIADLAV ELGLAGIVAT
NTTISRDGLK TPGAADLGAG GISGPPVARR ALEVLRRLYA RVGDKLVLIS VGGIETSDDA
WERITAGASL LQGYTGFVYG GGLWARSIND GVAARLRENG FGTLAEAVGS AAR
