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Protein

Dihydroorotate dehydrogenase (quinone)

Gene

pyrD

Organism
Alicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601)
Status
Unreviewed-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 annotationSAAS annotation

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:
  • FMNUniRule annotationNote: Binds 1 FMN per subunit.UniRule annotation
  • FMNNote: Binds 1 FMN per subunit.

Pathway: UMP biosynthesis via de novo pathway

This protein is involved in step 1 and 1 of the subpathway that synthesizes orotate from (S)-dihydroorotate (quinone route).UniRule annotationSAAS annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Dihydroorotate dehydrogenase (quinone) (pyrD), 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.

Pathway: UMP biosynthesis via de novo pathway

This protein is involved in step 1 and 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), 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 sitei69 – 691SubstrateUniRule annotation
Binding sitei89 – 891FMN; via amide nitrogenUniRule annotation
Binding sitei147 – 1471FMNUniRule annotation
Binding sitei180 – 1801FMNUniRule annotation
Binding sitei180 – 1801SubstrateUniRule annotation
Active sitei183 – 1831NucleophileUniRule annotation
Binding sitei185 – 1851SubstrateUniRule annotation
Binding sitei225 – 2251FMNUniRule annotation
Binding sitei253 – 2531FMN; via carbonyl oxygenUniRule annotation
Binding sitei276 – 2761FMN; via amide nitrogenUniRule annotation
Binding sitei305 – 3051FMN; via amide nitrogenUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi65 – 695FMNUniRule annotation
Nucleotide bindingi326 – 3272FMNUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

OxidoreductaseUniRule annotationSAAS annotation

Keywords - Biological processi

Pyrimidine biosynthesisUniRule annotationSAAS annotation

Keywords - Ligandi

Flavoprotein, FMNUniRule annotationSAAS annotation

Enzyme and pathway databases

BioCyciADEN596154:GHU6-2439-MONOMER.
UniPathwayiUPA00070; UER00946.
UPA00070; UER00946.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydroorotate dehydrogenase (quinone)UniRule annotationSAAS annotation (EC:1.3.5.2UniRule annotationSAAS annotation)
Alternative name(s):
DHOdehaseUniRule annotation
Dihydroorotate oxidaseUniRule annotation
Gene namesi
Name:pyrDUniRule annotation
Ordered Locus Names:Alide2_2408Imported
OrganismiAlicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601)Imported
Taxonomic identifieri596154 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeAlicycliphilus
ProteomesiUP000007938 Componenti: Chromosome

Subcellular locationi

  • Cell membrane UniRule annotationSAAS annotation; Peripheral membrane protein UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membraneUniRule annotationSAAS annotation, Membrane

Interactioni

Subunit structurei

Monomer.UniRule annotationSAAS annotation

Protein-protein interaction databases

STRINGi596154.Alide2_2408.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni114 – 1185Substrate bindingUniRule annotation
Regioni254 – 2552Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

KOiK00254.

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.

F4GCB3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLLPYAFAR PFLFGMDAEA AHELTMDMLA RGQRTPLQWA WCNETVSDPV
60 70 80 90 100
QLAGLTFPNR VGLAAGLDKN ARCIDALAAM GFGFVEVGTV TPKAQPGNPK
110 120 130 140 150
PRMFRLPEAR ALINRLGFNN EGLDAFIANV RRSQVRAQGK PLLLGLNIGK
160 170 180 190 200
NAATPIEQAT GDYLACLEGV YPHADYVTVN ISSPNTQNLR ALQSDEALDA
210 220 230 240 250
LLGAIADHRE KLAAAQGRRV PIFVKIAPDL NEAQVAVIAA TLTRHGMDGV
260 270 280 290 300
VATNTTIARD AVQGLPHAGE AGGLSGAPVR EASNAVIRQL RAALGPAFPI
310 320 330 340
VGVGGVMSAE DAVGKIRAGA DVVQIYTGLI YEGPALVSRA ARAIRAMR
Length:348
Mass (Da):36,742
Last modified:June 28, 2011 - v1
Checksum:i843DD28148E780DF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002657 Genomic DNA. Translation: AEB84772.1.
RefSeqiWP_013519048.1. NC_015422.1.
YP_004388288.1. NC_015422.1.

Genome annotation databases

EnsemblBacteriaiAEB84772; AEB84772; Alide2_2408.
KEGGiadk:Alide2_2408.
PATRICi54527494. VBIAliDen79014_2432.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002657 Genomic DNA. Translation: AEB84772.1.
RefSeqiWP_013519048.1. NC_015422.1.
YP_004388288.1. NC_015422.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi596154.Alide2_2408.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAEB84772; AEB84772; Alide2_2408.
KEGGiadk:Alide2_2408.
PATRICi54527494. VBIAliDen79014_2432.

Phylogenomic databases

KOiK00254.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00946.
UPA00070; UER00946.
BioCyciADEN596154:GHU6-2439-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. "Complete sequence of chromosome of Alicycliphilus denitrificans K601."
    US DOE Joint Genome Institute
    Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Peters L., Zeytun A., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Mikhailova N., Pagani I., Oosterkamp M.
    , Pieper D., van Berkel W., Langenhoff A., Smidt H., Stams A., Woyke T.
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 14773 / CIP 107495 / K601Imported.

Entry informationi

Entry nameiF4GCB3_ALIDK
AccessioniPrimary (citable) accession number: F4GCB3
Entry historyi
Integrated into UniProtKB/TrEMBL: June 28, 2011
Last sequence update: June 28, 2011
Last modified: June 24, 2015
This is version 29 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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.