PYRK_DESRM
ID PYRK_DESRM Reviewed; 262 AA.
AC A4J559;
DT 10-MAY-2017, 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(+)), electron transfer subunit {ECO:0000255|HAMAP-Rule:MF_01211};
DE AltName: Full=Dihydroorotate oxidase B, electron transfer subunit {ECO:0000255|HAMAP-Rule:MF_01211};
GN Name=pyrK {ECO:0000255|HAMAP-Rule:MF_01211};
GN OrderedLocusNames=Dred_1685 {ECO:0000312|EMBL:ABO50212.1};
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, SUBUNIT, COFACTOR, AND SUBCELLULAR 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: Responsible for channeling the electrons from the oxidation
CC of dihydroorotate from the FMN redox center in the PyrD type B subunit
CC to the ultimate electron acceptor NAD(+). {ECO:0000255|HAMAP-
CC Rule:MF_01211}.
CC -!- FUNCTION: Together with PyrD, 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 -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01211};
CC Note=Binds 1 FAD per subunit. {ECO:0000255|HAMAP-Rule:MF_01211};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01211,
CC ECO:0000305|PubMed:25389064};
CC Note=Binds 1 [2Fe-2S] cluster per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_01211};
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC orotate from (S)-dihydroorotate (NAD(+) route): step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_01211}.
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:0000255|HAMAP-Rule:MF_01211, ECO:0000269|PubMed:25389064}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:25389064}. Note=Was
CC recovered from both the soluble as well as the insoluble (presumably
CC membrane) protein fraction, and thus may be in some way also associated
CC with the membrane. {ECO:0000269|PubMed:25389064}.
CC -!- SIMILARITY: Belongs to the PyrK family. {ECO:0000255|HAMAP-
CC Rule:MF_01211}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CP000612; ABO50212.1; -; Genomic_DNA.
DR RefSeq; WP_011878027.1; NC_009253.1.
DR AlphaFoldDB; A4J559; -.
DR SMR; A4J559; -.
DR STRING; 349161.Dred_1685; -.
DR EnsemblBacteria; ABO50212; ABO50212; Dred_1685.
DR KEGG; drm:Dred_1685; -.
DR eggNOG; COG0543; Bacteria.
DR HOGENOM; CLU_003827_1_2_9; -.
DR OMA; RYMKCGI; -.
DR OrthoDB; 1885467at2; -.
DR UniPathway; UPA00070; UER00945.
DR Proteomes; UP000001556; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0009055; F:electron transfer activity; IEA:UniProtKB-UniRule.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 2.10.240.10; -; 1.
DR Gene3D; 3.40.50.80; -; 1.
DR HAMAP; MF_01211; DHODB_Fe_S_bind; 1.
DR InterPro; IPR008333; Cbr1-like_FAD-bd_dom.
DR InterPro; IPR012165; Cyt_c3_hydrogenase_gsu.
DR InterPro; IPR037117; Dihydroorotate_DH_ele_sf.
DR InterPro; IPR019480; Dihydroorotate_DH_Fe-S-bd.
DR InterPro; IPR023455; Dihydroorotate_DHASE_ETsu.
DR InterPro; IPR017927; FAD-bd_FR_type.
DR InterPro; IPR039261; FNR_nucleotide-bd.
DR InterPro; IPR001433; OxRdtase_FAD/NAD-bd.
DR InterPro; IPR017938; Riboflavin_synthase-like_b-brl.
DR Pfam; PF10418; DHODB_Fe-S_bind; 1.
DR Pfam; PF00970; FAD_binding_6; 1.
DR Pfam; PF00175; NAD_binding_1; 1.
DR PIRSF; PIRSF006816; Cyc3_hyd_g; 1.
DR SUPFAM; SSF52343; SSF52343; 1.
DR SUPFAM; SSF63380; SSF63380; 1.
DR PROSITE; PS51384; FAD_FR; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; Cytoplasm; Electron transport; FAD; Flavoprotein; Iron;
KW Iron-sulfur; Metal-binding; Pyrimidine biosynthesis; Reference proteome;
KW Transport.
FT CHAIN 1..262
FT /note="Dihydroorotate dehydrogenase B (NAD(+)), electron
FT transfer subunit"
FT /id="PRO_0000439794"
FT DOMAIN 2..102
FT /note="FAD-binding FR-type"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01211"
FT BINDING 53..56
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01211"
FT BINDING 70..72
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01211"
FT BINDING 77..78
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01211"
FT BINDING 224
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01211"
FT BINDING 229
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01211"
FT BINDING 232
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01211"
FT BINDING 248
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01211"
SQ SEQUENCE 262 AA; 28456 MW; 43771C4DB6962623 CRC64;
MSKVFDAKVL AVYMVAPNTY YMEFDAPDIA RLAVPGQFVH VRCGETNDPL LRRPISIHMV
SRPKGVLALL FRVVGKGTEI LSQQKPGDRV NMMGPLGRGF TLPLPGSKVA VAAGGIGAAP
LVFLVQELAN IKCQVTVYLG ARDKRSILCD GQFIQMEAEV VIATDDGSLG FKGTVPELMK
RHMDWRKTAM TYVCGPGIMM KEISTMLAEA DVPGEVSLEE RMGCGVGACL SCAVKISHHG
QISNKRACFE GPVFPSWQVV WE
