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Protein

Dihydroorotate dehydrogenase (quinone)

Gene

pyrD

Organism
Escherichia coli O9:H4 (strain HS)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor.UniRule annotation

Catalytic activityi

(S)-dihydroorotate + a quinone = orotate + a quinol.UniRule annotation

Cofactori

FMNUniRule annotationNote: Binds 1 FMN per subunit.UniRule annotation

Pathway:iUMP biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes orotate from (S)-dihydroorotate (quinone route).UniRule annotation
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 – 661SubstrateUniRule annotation
Binding sitei86 – 861FMN; via amide nitrogenUniRule annotation
Binding sitei139 – 1391FMNUniRule annotation
Binding sitei172 – 1721FMNUniRule annotation
Binding sitei172 – 1721SubstrateUniRule annotation
Active sitei175 – 1751NucleophileUniRule annotation
Binding sitei177 – 1771SubstrateUniRule annotation
Binding sitei217 – 2171FMNUniRule annotation
Binding sitei245 – 2451FMN; via carbonyl oxygenUniRule annotation
Binding sitei268 – 2681FMN; via amide nitrogenUniRule annotation
Binding sitei297 – 2971FMN; via amide nitrogenUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi62 – 665FMNUniRule annotation
Nucleotide bindingi318 – 3192FMNUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyrimidine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BioCyciECOL331112:GHHI-1048-MONOMER.
UniPathwayiUPA00070; UER00946.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydroorotate dehydrogenase (quinone)UniRule annotation (EC:1.3.5.2UniRule annotation)
Alternative name(s):
DHOdehaseUniRule annotation
Short name:
DHODUniRule annotation
Short name:
DHODaseUniRule annotation
Dihydroorotate oxidaseUniRule annotation
Gene namesi
Name:pyrDUniRule annotation
Ordered Locus Names:EcHS_A1054
OrganismiEscherichia coli O9:H4 (strain HS)
Taxonomic identifieri331112 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Subcellular locationi

  • Cell membrane UniRule annotation; Peripheral membrane protein UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 336336Dihydroorotate dehydrogenase (quinone)PRO_1000058682Add
BLAST

Proteomic databases

PRIDEiA7ZYP7.

Interactioni

Subunit structurei

Monomer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliA7ZYP7.
SMRiA7ZYP7. Positions 1-336.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the dihydroorotate dehydrogenase family. Type 2 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG0167.
HOGENOMiHOG000225103.
OMAiAECIDAF.
OrthoDBiEOG65BDN8.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00225. DHO_dh_type2.
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.

A7ZYP7-1 [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:October 23, 2007 - v1
Checksum:i973227EAE6B83622
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000802 Genomic DNA. Translation: ABV05401.1.

Genome annotation databases

EnsemblBacteriaiABV05401; ABV05401; EcHS_A1054.
PATRICi18312092. VBIEscCol77814_1023.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000802 Genomic DNA. Translation: ABV05401.1.

3D structure databases

ProteinModelPortaliA7ZYP7.
SMRiA7ZYP7. Positions 1-336.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiA7ZYP7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABV05401; ABV05401; EcHS_A1054.
PATRICi18312092. VBIEscCol77814_1023.

Phylogenomic databases

eggNOGiCOG0167.
HOGENOMiHOG000225103.
OMAiAECIDAF.
OrthoDBiEOG65BDN8.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00946.
BioCyciECOL331112:GHHI-1048-MONOMER.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00225. DHO_dh_type2.
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...

Publicationsi

  1. "The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates."
    Rasko D.A., Rosovitz M.J., Myers G.S.A., Mongodin E.F., Fricke W.F., Gajer P., Crabtree J., Sebaihia M., Thomson N.R., Chaudhuri R., Henderson I.R., Sperandio V., Ravel J.
    J. Bacteriol. 190:6881-6893(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HS.

Entry informationi

Entry nameiPYRD_ECOHS
AccessioniPrimary (citable) accession number: A7ZYP7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: October 23, 2007
Last modified: July 22, 2015
This is version 58 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.