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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei66 – 661Substrate
Binding sitei86 – 861FMN; via amide nitrogen1 Publication
Binding sitei139 – 1391FMN1 Publication
Binding sitei172 – 1721FMN1 Publication
Binding sitei172 – 1721Substrate
Active sitei175 – 1751Nucleophile
Binding sitei177 – 1771Substrate
Binding sitei217 – 2171FMN1 Publication
Binding sitei245 – 2451FMN; via carbonyl oxygen1 Publication
Binding sitei268 – 2681FMN; via amide nitrogen1 Publication
Binding sitei297 – 2971FMN; via amide nitrogen1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi62 – 665FMN1 Publication
Nucleotide bindingi318 – 3192FMN1 Publication

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi175 – 1751S → A: Almost no activity. 1 Publication
Mutagenesisi175 – 1751S → C: 500-fold reduction in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 336336Dihydroorotate dehydrogenase (quinone)PRO_0000148437Add
BLAST

Proteomic databases

PaxDbiP0A7E1.
PRIDEiP0A7E1.

2D gel databases

SWISS-2DPAGEP0A7E1.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4259440. 19 interactions.
849930. 1 interaction.
DIPiDIP-35945N.
IntActiP0A7E1. 6 interactions.
STRINGi511145.b0945.

Structurei

Secondary structure

1
336
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 108Combined sources
Helixi15 – 2915Combined sources
Helixi33 – 375Combined sources
Beta strandi47 – 493Combined sources
Beta strandi52 – 609Combined sources
Helixi71 – 766Combined sources
Beta strandi80 – 878Combined sources
Beta strandi100 – 1034Combined sources
Turni104 – 1074Combined sources
Beta strandi108 – 1114Combined sources
Helixi120 – 12910Combined sources
Beta strandi134 – 1407Combined sources
Helixi148 – 1514Combined sources
Helixi152 – 16211Combined sources
Helixi163 – 1653Combined sources
Beta strandi167 – 1726Combined sources
Beta strandi176 – 1783Combined sources
Helixi181 – 1855Combined sources
Helixi187 – 20822Combined sources
Beta strandi214 – 2174Combined sources
Helixi224 – 23613Combined sources
Beta strandi240 – 2445Combined sources
Turni258 – 2614Combined sources
Beta strandi263 – 2686Combined sources
Helixi269 – 2713Combined sources
Helixi272 – 28615Combined sources
Beta strandi292 – 2976Combined sources
Helixi301 – 31010Combined sources
Beta strandi313 – 3186Combined sources
Helixi319 – 3246Combined sources
Helixi326 – 33510Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP0A7E1.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni111 – 1155Substrate binding
Regioni246 – 2472Substrate binding

Sequence similaritiesi

Phylogenomic databases

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

Family and domain databases

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1F76X-ray2.50A/B/D/E1-336[»]
ProteinModelPortaliP0A7E1.
SMRiP0A7E1. Positions 1-336.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259440. 19 interactions.
849930. 1 interaction.
DIPiDIP-35945N.
IntActiP0A7E1. 6 interactions.
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

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: September 7, 2016
This is version 105 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.