PYRD_ORYSJ
ID PYRD_ORYSJ Reviewed; 469 AA.
AC Q7XKC8; A0A0P0WG90; Q0J918; Q9FZM9;
DT 24-JUL-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2003, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Dihydroorotate dehydrogenase (quinone), mitochondrial;
DE Short=DHOdehase;
DE EC=1.3.5.2;
DE AltName: Full=Dihydroorotate oxidase;
DE Flags: Precursor;
GN Name=PYRD; OrderedLocusNames=Os04g0676300, LOC_Os04g57950;
GN ORFNames=OsJ_16613, OSJNBa0064G10.3;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Ito Y.;
RT "Oryza sativa dihydroorotate dehydrogenase gene, complete cds.";
RL Submitted (FEB-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Leaf;
RA Wang M.M.;
RT "Cloning of a cDNA for senescence-related protein from Oryza sativa.";
RL Submitted (OCT-2005) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447439; DOI=10.1038/nature01183;
RA Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y.,
RA Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S., Tang Y., Weng Q.,
RA Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T.,
RA Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R.,
RA Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G.,
RA Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C.,
RA Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J.,
RA Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J.,
RA Li J., Hong G., Xue Y., Han B.;
RT "Sequence and analysis of rice chromosome 4.";
RL Nature 420:316-320(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [6]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC quinone as electron acceptor. {ECO:0000250}.
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 -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Note=Binds 1 FMN per subunit.;
CC -!- PATHWAY: Pyrimidine metabolism; UMP biosynthesis via de novo pathway;
CC orotate from (S)-dihydroorotate (quinone route): step 1/1.
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane {ECO:0000305};
CC Single-pass membrane protein {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the dihydroorotate dehydrogenase family. Type 2
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB11988.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAF16169.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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; AB038557; BAB11988.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DQ269457; ABB76659.1; -; mRNA.
DR EMBL; AL606668; CAE05752.1; -; Genomic_DNA.
DR EMBL; AP008210; BAF16169.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014960; BAS91623.1; -; Genomic_DNA.
DR EMBL; CM000141; EAZ32402.1; -; Genomic_DNA.
DR RefSeq; XP_015633939.1; XM_015778453.1.
DR AlphaFoldDB; Q7XKC8; -.
DR SMR; Q7XKC8; -.
DR STRING; 4530.OS04T0676300-01; -.
DR PaxDb; Q7XKC8; -.
DR PRIDE; Q7XKC8; -.
DR EnsemblPlants; Os04t0676300-01; Os04t0676300-01; Os04g0676300.
DR GeneID; 4337396; -.
DR Gramene; Os04t0676300-01; Os04t0676300-01; Os04g0676300.
DR KEGG; osa:4337396; -.
DR eggNOG; KOG1436; Eukaryota.
DR HOGENOM; CLU_013640_0_0_1; -.
DR InParanoid; Q7XKC8; -.
DR OMA; ERIKMGA; -.
DR OrthoDB; 1194348at2759; -.
DR UniPathway; UPA00070; UER00946.
DR Proteomes; UP000000763; Chromosome 4.
DR Proteomes; UP000007752; Chromosome 4.
DR Proteomes; UP000059680; Chromosome 4.
DR Genevisible; Q7XKC8; OS.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005743; C:mitochondrial inner membrane; IBA:GO_Central.
DR GO; GO:0004152; F:dihydroorotate dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0006207; P:'de novo' pyrimidine nucleobase biosynthetic process; IBA:GO_Central.
DR GO; GO:0044205; P:'de novo' UMP biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0009220; P:pyrimidine ribonucleotide biosynthetic process; IBA:GO_Central.
DR CDD; cd04738; DHOD_2_like; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR005720; Dihydroorotate_DH.
DR InterPro; IPR005719; Dihydroorotate_DH_2.
DR InterPro; IPR001295; Dihydroorotate_DH_CS.
DR Pfam; PF01180; DHO_dh; 1.
DR TIGRFAMs; TIGR01036; pyrD_sub2; 1.
DR PROSITE; PS00911; DHODEHASE_1; 1.
DR PROSITE; PS00912; DHODEHASE_2; 1.
PE 2: Evidence at transcript level;
KW Flavoprotein; FMN; Membrane; Mitochondrion; Mitochondrion inner membrane;
KW Oxidoreductase; Reference proteome; Transit peptide; Transmembrane;
KW Transmembrane helix.
FT TRANSIT 1..37
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 38..469
FT /note="Dihydroorotate dehydrogenase (quinone),
FT mitochondrial"
FT /id="PRO_0000423080"
FT TRANSMEM 62..82
FT /note="Helical"
FT /evidence="ECO:0000255"
FT REGION 219..247
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 286
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 150..154
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 154
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 174
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 199..203
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 252
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 283..288
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 283
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 328
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 356
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 357..358
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 380
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 409
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 430..431
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
SQ SEQUENCE 469 AA; 49534 MW; F1DA357D03BFEC41 CRC64;
MSSSAAALAW RRSLRDALLR GSAWRGAPAA NSAAARLAST ASASEAAAGP KKVPPPPRKG
RLLTGAMIGL AIAGGAYVST ADEAKFCGWL FKSTQLVNPL FALLDAEFAH RLAVTAASHG
FVPREKRPDP SVLGLEIWGR KFTNPIGLAA GFDKNAEAVE GLLGMGFGFV EVGSVTPLPQ
EGNPKPRIFR LREHGAVINR CGFNSEGIVV VAKRLGAQHG KRKMEETSSS TSPTTSDVKQ
GGKAGPGILG VNLGKNKISE DATADYVQGV HTLSQYADYL VINVSSPNTP GLRKLQGRKQ
LKDLVKKVQA ARDEMQWAED GPPPLLVKIA PDLSKQDLED IAAVALALRL DGLIISNTTI
SRPSPADTHP LAQEAGGLSG KPLFDLSTNV LREMYILTRG KIPLIGCGGV SSGEDAYKKI
RSGATLVQLY TAFAYGGPAL IPRIKAELAE CLERDGFKSV QEAVGADFK
