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Protein

Dihydroorotate dehydrogenase (quinone)

Gene

pyrD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor.1 Publication

Catalytic activityi

(S)-dihydroorotate + a quinone = orotate + a quinol.1 Publication

Cofactori

FMN1 PublicationNote: Binds 1 FMN per subunit.1 Publication

Kineticsi

  1. KM=28.8 µM for dihydroorotate1 Publication
  1. Vmax=180 µmol/min/mg enzyme1 Publication

Pathwayi: UMP biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes orotate from (S)-dihydroorotate (quinone route).
Proteins known to be involved in this subpathway in this organism are:
  1. Dihydroorotate dehydrogenase (quinone) (pyrD)
This subpathway is part of the pathway UMP biosynthesis via de novo pathway, which is itself part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes orotate from (S)-dihydroorotate (quinone route), the pathway UMP biosynthesis via de novo pathway and in Pyrimidine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei66Substrate1
Binding sitei86FMN; via amide nitrogen1 Publication1
Binding sitei139FMN1 Publication1
Binding sitei172FMN1 Publication1
Binding sitei172Substrate1
Active sitei175Nucleophile1
Binding sitei177Substrate1
Binding sitei217FMN1 Publication1
Binding sitei245FMN; via carbonyl oxygen1 Publication1
Binding sitei268FMN; via amide nitrogen1 Publication1
Binding sitei297FMN; via amide nitrogen1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi62 – 66FMN1 Publication5
Nucleotide bindingi318 – 319FMN1 Publication2

GO - Molecular functioni

  • dihydroorotate dehydrogenase activity Source: EcoCyc
  • FMN binding Source: EcoCyc

GO - Biological processi

  • 'de novo' pyrimidine nucleobase biosynthetic process Source: EcoCyc
  • 'de novo' UMP biosynthetic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyrimidine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BioCyciEcoCyc:DIHYDROOROTOX-MONOMER.
ECOL316407:JW0928-MONOMER.
MetaCyc:DIHYDROOROTOX-MONOMER.
BRENDAi1.3.5.2. 2026.
SABIO-RKP0A7E1.
UniPathwayiUPA00070; UER00946.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydroorotate dehydrogenase (quinone) (EC:1.3.5.2)
Alternative name(s):
DHOdehase
Short name:
DHOD
Short name:
DHODase
Dihydroorotate oxidase
Gene namesi
Name:pyrD
Ordered Locus Names:b0945, JW0928
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10807. pyrD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • membrane Source: EcoCyc
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi175S → A: Almost no activity. 1 Publication1
Mutagenesisi175S → C: 500-fold reduction in activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001484371 – 336Dihydroorotate dehydrogenase (quinone)Add BLAST336

Proteomic databases

PaxDbiP0A7E1.
PRIDEiP0A7E1.

2D gel databases

SWISS-2DPAGEP0A7E1.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4259440. 19 interactors.
849930. 1 interactor.
DIPiDIP-35945N.
IntActiP0A7E1. 6 interactors.
STRINGi511145.b0945.

Structurei

Secondary structure

1336
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 10Combined sources8
Helixi15 – 29Combined sources15
Helixi33 – 37Combined sources5
Beta strandi47 – 49Combined sources3
Beta strandi52 – 60Combined sources9
Helixi71 – 76Combined sources6
Beta strandi80 – 87Combined sources8
Beta strandi100 – 103Combined sources4
Turni104 – 107Combined sources4
Beta strandi108 – 111Combined sources4
Helixi120 – 129Combined sources10
Beta strandi134 – 140Combined sources7
Helixi148 – 151Combined sources4
Helixi152 – 162Combined sources11
Helixi163 – 165Combined sources3
Beta strandi167 – 172Combined sources6
Beta strandi176 – 178Combined sources3
Helixi181 – 185Combined sources5
Helixi187 – 208Combined sources22
Beta strandi214 – 217Combined sources4
Helixi224 – 236Combined sources13
Beta strandi240 – 244Combined sources5
Turni258 – 261Combined sources4
Beta strandi263 – 268Combined sources6
Helixi269 – 271Combined sources3
Helixi272 – 286Combined sources15
Beta strandi292 – 297Combined sources6
Helixi301 – 310Combined sources10
Beta strandi313 – 318Combined sources6
Helixi319 – 324Combined sources6
Helixi326 – 335Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1F76X-ray2.50A/B/D/E1-336[»]
ProteinModelPortaliP0A7E1.
SMRiP0A7E1.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A7E1.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni111 – 115Substrate binding5
Regioni246 – 247Substrate binding2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107QYT. Bacteria.
COG0167. LUCA.
HOGENOMiHOG000225103.
InParanoidiP0A7E1.
KOiK00254.
OMAiERIKMGA.
PhylomeDBiP0A7E1.

Family and domain databases

CDDicd04738. DHOD_2_like. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00225. DHO_dh_type2. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR005720. Dihydroorotate_DH.
IPR012135. Dihydroorotate_DH_1_2.
IPR005719. Dihydroorotate_DH_2.
IPR001295. Dihydroorotate_DH_CS.
[Graphical view]
PfamiPF01180. DHO_dh. 1 hit.
[Graphical view]
PIRSFiPIRSF000164. DHO_oxidase. 1 hit.
TIGRFAMsiTIGR01036. pyrD_sub2. 1 hit.
PROSITEiPS00911. DHODEHASE_1. 1 hit.
PS00912. DHODEHASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A7E1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYYPFVRKAL FQLDPERAHE FTFQQLRRIT GTPFEALVRQ KVPAKPVNCM
60 70 80 90 100
GLTFKNPLGL AAGLDKDGEC IDALGAMGFG SIEIGTVTPR PQPGNDKPRL
110 120 130 140 150
FRLVDAEGLI NRMGFNNLGV DNLVENVKKA HYDGVLGINI GKNKDTPVEQ
160 170 180 190 200
GKDDYLICME KIYAYAGYIA INISSPNTPG LRTLQYGEAL DDLLTAIKNK
210 220 230 240 250
QNDLQAMHHK YVPIAVKIAP DLSEEELIQV ADSLVRHNID GVIATNTTLD
260 270 280 290 300
RSLVQGMKNC DQTGGLSGRP LQLKSTEIIR RLSLELNGRL PIIGVGGIDS
310 320 330
VIAAREKIAA GASLVQIYSG FIFKGPPLIK EIVTHI
Length:336
Mass (Da):36,775
Last modified:August 13, 1987 - v1
Checksum:i973227EAE6B83622
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02826 Genomic DNA. Translation: CAA26594.1.
U00096 Genomic DNA. Translation: AAC74031.1.
AP009048 Genomic DNA. Translation: BAA35700.1.
PIRiA23109. DEECDO.
RefSeqiNP_415465.1. NC_000913.3.
WP_001295352.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74031; AAC74031; b0945.
BAA35700; BAA35700; BAA35700.
GeneIDi945556.
KEGGiecj:JW0928.
eco:b0945.
PATRICi32117109. VBIEscCol129921_0979.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02826 Genomic DNA. Translation: CAA26594.1.
U00096 Genomic DNA. Translation: AAC74031.1.
AP009048 Genomic DNA. Translation: BAA35700.1.
PIRiA23109. DEECDO.
RefSeqiNP_415465.1. NC_000913.3.
WP_001295352.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1F76X-ray2.50A/B/D/E1-336[»]
ProteinModelPortaliP0A7E1.
SMRiP0A7E1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259440. 19 interactors.
849930. 1 interactor.
DIPiDIP-35945N.
IntActiP0A7E1. 6 interactors.
STRINGi511145.b0945.

2D gel databases

SWISS-2DPAGEP0A7E1.

Proteomic databases

PaxDbiP0A7E1.
PRIDEiP0A7E1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74031; AAC74031; b0945.
BAA35700; BAA35700; BAA35700.
GeneIDi945556.
KEGGiecj:JW0928.
eco:b0945.
PATRICi32117109. VBIEscCol129921_0979.

Organism-specific databases

EchoBASEiEB0800.
EcoGeneiEG10807. pyrD.

Phylogenomic databases

eggNOGiENOG4107QYT. Bacteria.
COG0167. LUCA.
HOGENOMiHOG000225103.
InParanoidiP0A7E1.
KOiK00254.
OMAiERIKMGA.
PhylomeDBiP0A7E1.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00946.
BioCyciEcoCyc:DIHYDROOROTOX-MONOMER.
ECOL316407:JW0928-MONOMER.
MetaCyc:DIHYDROOROTOX-MONOMER.
BRENDAi1.3.5.2. 2026.
SABIO-RKP0A7E1.

Miscellaneous databases

EvolutionaryTraceiP0A7E1.
PROiP0A7E1.

Family and domain databases

CDDicd04738. DHOD_2_like. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00225. DHO_dh_type2. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR005720. Dihydroorotate_DH.
IPR012135. Dihydroorotate_DH_1_2.
IPR005719. Dihydroorotate_DH_2.
IPR001295. Dihydroorotate_DH_CS.
[Graphical view]
PfamiPF01180. DHO_dh. 1 hit.
[Graphical view]
PIRSFiPIRSF000164. DHO_oxidase. 1 hit.
TIGRFAMsiTIGR01036. pyrD_sub2. 1 hit.
PROSITEiPS00911. DHODEHASE_1. 1 hit.
PS00912. DHODEHASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPYRD_ECOLI
AccessioniPrimary (citable) accession number: P0A7E1
Secondary accession number(s): P05021
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: November 2, 2016
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.