PYRDB_DESRM
ID PYRDB_DESRM Reviewed; 304 AA.
AC A4J560;
DT 20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2007, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit {ECO:0000305};
DE Short=DHOD B {ECO:0000305};
DE Short=DHODase B {ECO:0000305};
DE Short=DHOdehase B {ECO:0000305};
DE EC=1.3.1.14 {ECO:0000250|UniProtKB:P54322};
DE AltName: Full=Dihydroorotate oxidase B;
DE AltName: Full=Orotate reductase (NADH);
GN Name=pyrD; OrderedLocusNames=Dred_1686;
OS Desulforamulus reducens (strain ATCC BAA-1160 / DSM 100696 / MI-1)
OS (Desulfotomaculum reducens).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Peptococcaceae;
OC Desulforamulus.
OX NCBI_TaxID=349161;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1160 / DSM 100696 / MI-1;
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 Sims D., Brettin T., Bruce D., Han C., Tapia R., Schmutz J., Larimer F.,
RA Land M., Hauser L., Kyrpides N., Kim E., Tebo B.M., Richardson P.;
RT "Complete sequence of Desulfotomaculum reducens MI-1.";
RL Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION, METAL REDUCTASE ACTIVITY, COFACTOR, SUBUNIT, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=ATCC BAA-1160 / DSM 100696 / MI-1;
RX PubMed=25389064; DOI=10.1111/1462-2920.12673;
RA Otwell A.E., Sherwood R.W., Zhang S., Nelson O.D., Li Z., Lin H.,
RA Callister S.J., Richardson R.E.;
RT "Identification of proteins capable of metal reduction from the proteome of
RT the Gram-positive bacterium Desulfotomaculum reducens MI-1 using an NADH-
RT based activity assay.";
RL Environ. Microbiol. 17:1977-1990(2015).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC NAD(+) as electron acceptor. {ECO:0000250|UniProtKB:P54322}.
CC -!- FUNCTION: Together with PyrK, also forms a metal reductase complex able
CC to reduce Fe(III)-chelates to Fe(II)-chelates, as well as soluble
CC Cr(VI) and U(VI), using NADH as electron donor. To a lesser extent, can
CC also use NADPH as an electron donor. Is unable to reduce riboflavin and
CC FMN with NADH as electron donor. May have an in vivo role in metal
CC reduction in D.reducens, which is an organism capable of reducing
CC contaminant heavy metals and radionuclides.
CC {ECO:0000269|PubMed:25389064}.
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 Evidence={ECO:0000250|UniProtKB:P54322};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000250|UniProtKB:P54322, ECO:0000305|PubMed:25389064};
CC Note=Binds 1 FMN per subunit. {ECO:0000250|UniProtKB:P54322};
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 (By
CC similarity). However, the metal reductase complex seems to be composed
CC of a heterooctamer of 4 PyrK and 4 PyrD subunits (PubMed:25389064).
CC {ECO:0000250|UniProtKB:P54322, ECO:0000269|PubMed:25389064}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00224,
CC ECO:0000305|PubMed:25389064}. Note=Was recovered from both the soluble
CC as well as the insoluble (presumably membrane) protein fraction, and
CC thus may be in some way also associated with the membrane.
CC {ECO:0000269|PubMed:25389064}.
CC -!- SIMILARITY: Belongs to the dihydroorotate dehydrogenase family. Type 1
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_00224}.
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DR EMBL; CP000612; ABO50213.1; -; Genomic_DNA.
DR RefSeq; WP_011878028.1; NC_009253.1.
DR AlphaFoldDB; A4J560; -.
DR SMR; A4J560; -.
DR STRING; 349161.Dred_1686; -.
DR EnsemblBacteria; ABO50213; ABO50213; Dred_1686.
DR KEGG; drm:Dred_1686; -.
DR eggNOG; COG0167; Bacteria.
DR HOGENOM; CLU_042042_0_0_9; -.
DR OMA; SCPHAKG; -.
DR OrthoDB; 1109542at2; -.
DR UniPathway; UPA00070; UER00945.
DR Proteomes; UP000001556; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004152; F:dihydroorotate dehydrogenase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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 1: Evidence at protein level;
KW Cytoplasm; Flavoprotein; FMN; Metal-binding; NAD; Oxidoreductase;
KW Pyrimidine biosynthesis; Reference proteome.
FT CHAIN 1..304
FT /note="Dihydroorotate dehydrogenase B (NAD(+)), catalytic
FT subunit"
FT /id="PRO_0000336443"
FT ACT_SITE 131
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 22
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 46..47
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 46
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 70..74
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 100
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 128
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 128
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 166
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 192
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 193..194
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 218
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 244..245
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
FT BINDING 266..267
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00224"
SQ SEQUENCE 304 AA; 31975 MW; A7D6142318E99F77 CRC64;
MKLNLAVKIG QLDMINPVTT ASGTFGYGQE YSPYVDLNQL GAIVVKGTTL EPREGNPTPR
LVETPSGILN SIGLQNSGVD YLLEHYVPFF KKLQTNVIVN ISGNTAEEYG QLAARLDEAD
GIAALEVNIS CPNVKKGGMA FGGDFRTAAE VTKVVKNSTA LPVIVKLSPN VTDIAEIARA
VEGAGADGLS VINTLLGMAI DVRKRKPVLG NTMGGLSGPA VKPVALRAVW QVYKAVHIPI
IGMGGIMNAT DALEFILAGA QAVSVGTANF VNPYATKEII QGMEKYLMEN GIGDINELVG
AAHL
