PYRD_ARATH
ID PYRD_ARATH Reviewed; 460 AA.
AC P32746; Q0WRX8; Q9FMX1;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2002, sequence version 2.
DT 03-AUG-2022, entry version 163.
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=At5g23300; ORFNames=MKD15.16;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=1303803; DOI=10.1111/j.1365-313x.1992.00417.x;
RA Minet M., Dufour M.E., Lacroute F.;
RT "Complementation of Saccharomyces cerevisiae auxotrophic mutants by
RT Arabidopsis thaliana cDNAs.";
RL Plant J. 2:417-422(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=12372626; DOI=10.1016/s0014-5793(02)03425-7;
RA Ullrich A., Knecht W., Piskur J., Loeffler M.;
RT "Plant dihydroorotate dehydrogenase differs significantly in substrate
RT specificity and inhibition from the animal enzymes.";
RL FEBS Lett. 529:346-350(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9501997; DOI=10.1093/dnares/4.6.401;
RA Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT features of the regions of 1,191,918 bp covered by seventeen physically
RT assigned P1 clones.";
RL DNA Res. 4:401-414(1997).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF Clones.";
RL Submitted (AUG-2006) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14671022; DOI=10.1105/tpc.016055;
RA Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
RA Millar A.H.;
RT "Experimental analysis of the Arabidopsis mitochondrial proteome highlights
RT signaling and regulatory components, provides assessment of targeting
RT prediction programs, and indicates plant-specific mitochondrial proteins.";
RL Plant Cell 16:241-256(2004).
CC -!- FUNCTION: Catalyzes the conversion of dihydroorotate to orotate with
CC quinone as electron acceptor.
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:0000269|PubMed:12372626};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Note=Binds 1 FMN per subunit.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=40 uM for dihydroorotate {ECO:0000269|PubMed:12372626};
CC KM=112 uM for decylubiquinone {ECO:0000269|PubMed:12372626};
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:12372626};
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=BAB11185.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAA44695.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; X62909; CAA44695.1; ALT_FRAME; mRNA.
DR EMBL; AF454729; AAN64025.1; -; mRNA.
DR EMBL; AB007648; BAB11185.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED93149.1; -; Genomic_DNA.
DR EMBL; AK228165; BAF00121.1; -; mRNA.
DR EMBL; BT026524; ABH04631.1; -; mRNA.
DR PIR; S23762; S23762.
DR RefSeq; NP_568428.1; NM_122236.3.
DR AlphaFoldDB; P32746; -.
DR SMR; P32746; -.
DR STRING; 3702.AT5G23300.1; -.
DR MetOSite; P32746; -.
DR SwissPalm; P32746; -.
DR PaxDb; P32746; -.
DR PRIDE; P32746; -.
DR ProteomicsDB; 224822; -.
DR EnsemblPlants; AT5G23300.1; AT5G23300.1; AT5G23300.
DR GeneID; 832394; -.
DR Gramene; AT5G23300.1; AT5G23300.1; AT5G23300.
DR KEGG; ath:AT5G23300; -.
DR Araport; AT5G23300; -.
DR TAIR; locus:2166943; AT5G23300.
DR eggNOG; KOG1436; Eukaryota.
DR HOGENOM; CLU_013640_0_0_1; -.
DR InParanoid; P32746; -.
DR OMA; ERIKMGA; -.
DR OrthoDB; 1194348at2759; -.
DR PhylomeDB; P32746; -.
DR BioCyc; ARA:AT5G23300-MON; -.
DR BioCyc; MetaCyc:AT5G23300-MON; -.
DR BRENDA; 1.3.5.2; 399.
DR UniPathway; UPA00070; UER00946.
DR PRO; PR:P32746; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; P32746; baseline and differential.
DR Genevisible; P32746; AT.
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:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0004152; F:dihydroorotate dehydrogenase activity; IDA:TAIR.
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; IDA:TAIR.
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 1: Evidence at protein level;
KW Flavoprotein; FMN; Membrane; Mitochondrion; Mitochondrion inner membrane;
KW Oxidoreductase; Pyrimidine biosynthesis; Reference proteome;
KW Transit peptide; Transmembrane; Transmembrane helix.
FT TRANSIT 1..32
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 33..460
FT /note="Dihydroorotate dehydrogenase (quinone),
FT mitochondrial"
FT /id="PRO_0000029889"
FT TRANSMEM 53..69
FT /note="Helical"
FT /evidence="ECO:0000255"
FT REGION 213..245
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 215..229
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 277
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 141..145
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 145
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 165
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 190..194
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 243
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 274..279
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 274
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 319
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 347
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 348..349
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 371
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 400
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
FT BINDING 421..422
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250"
SQ SEQUENCE 460 AA; 48547 MW; E8DF1C6CCEA44FFD CRC64;
MAGRAATSSA KWAREFLFRR VSSNPLGATR NCSSVPGASS APKVPHFSKR GRILTGATIG
LAIAGGAYVS TADEATFCGW LFNATKVVNP FFALLDAEFA HKLAVSAAAR GWVPREKRPD
PAILGLEVWG RKFSNPIGLA AGFDKNAEAT EGLLGMGFGF VEVGSVTPVP QEGNPKPRIF
RLSQEGAIIN RCGFNSEGIV VVAKRLGAQH GKRMLAETSA TSSSPSDDVK PGGKSGPGIL
GVNLGKNKTS EDAAADYVQG VHNLSQYADY LVINVSSPNT AGLRMLQGRK QLKDLVKKVQ
AARDEMQWGD EGPPPLLVKI APDLSRGELE DIAAVALALH LDGLIISNTT VSRPDAVSNN
PVATETGGLS GKPLFALSTN MLRDMYTLTR GKIPLIGCGG VSSGEDAYKK IRAGATLVQL
YTGFAYGGPA LIPQIKEELV KCLERDGFKS IHEAIGADHR
