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Protein

Dihydroorotate dehydrogenase (quinone)

Gene

pyrD

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
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.By similarity

Catalytic activityi

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

Cofactori

FMNBy similarityNote: Binds 1 FMN per subunit.By similarity

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 sitei71SubstrateBy similarity1
Binding sitei91FMN; via amide nitrogenBy similarity1
Binding sitei145FMNBy similarity1
Binding sitei178FMNBy similarity1
Binding sitei178SubstrateBy similarity1
Active sitei181NucleophileBy similarity1
Binding sitei183SubstrateBy similarity1
Binding sitei214FMNBy similarity1
Binding sitei242FMN; via carbonyl oxygenBy similarity1
Binding sitei262FMN; via amide nitrogenBy similarity1
Binding sitei291FMN; via amide nitrogenBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi67 – 71FMNBy similarity5
Nucleotide bindingi312 – 313FMNBy similarity2

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

BioCyciHPY:HP1011-MONOMER.
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:HP_1011
OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Taxonomic identifieri85962 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
Proteomesi
  • UP000000429 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001484451 – 351Dihydroorotate dehydrogenase (quinone)Add BLAST351

Proteomic databases

PaxDbiO25655.

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

STRINGi85962.HP1011.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LX3model-A1-351[»]
ProteinModelPortaliO25655.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni116 – 120Substrate bindingBy similarity5
Regioni243 – 244Substrate bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107QYT. Bacteria.
COG0167. LUCA.
KOiK00254.
OMAiERIKMGA.

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.

O25655-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLYSLVKKYL FSLDAEDAHE KVCKILRMLS SSPFLCNLID SQWGYQNPKL
60 70 80 90 100
ENEILGLHFP NPLGLAAGFD KNASMLRALM AFGFGYLEAG TLTNEAQVGN
110 120 130 140 150
ERPRLFRHIE EESLQNAMGF NNYGAILGVR SFKRFAPYKT PIGINLGKNK
160 170 180 190 200
HIEQAHALED YKAVLSKCLN IGDYYTFNLS SPNTPNLRDL QNKAFVHELF
210 220 230 240 250
CMAKEMTHKP LFLKIAPDLE TDDMLEIVNS AIGAGAHGII ATNTTIDKSL
260 270 280 290 300
VFAPKEMGGL SGKCLTKKSR EIFKELAKAF FNKSVLVSVG GISDAKEAYE
310 320 330 340 350
RIKMGASLLQ IYSAFIYNGP NLCQNILKDL VKLLQKDGFL SVKEAIGADL

R
Length:351
Mass (Da):39,002
Last modified:January 1, 1998 - v1
Checksum:i784D32A23A36F20C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD08055.1.
PIRiC64646.
RefSeqiNP_207801.1. NC_000915.1.
WP_000967190.1. NC_018939.1.

Genome annotation databases

EnsemblBacteriaiAAD08055; AAD08055; HP_1011.
GeneIDi899546.
KEGGiheo:C694_05235.
hpy:HP1011.
PATRICi20593357. VBIHelPyl33062_1059.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD08055.1.
PIRiC64646.
RefSeqiNP_207801.1. NC_000915.1.
WP_000967190.1. NC_018939.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LX3model-A1-351[»]
ProteinModelPortaliO25655.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi85962.HP1011.

Proteomic databases

PaxDbiO25655.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD08055; AAD08055; HP_1011.
GeneIDi899546.
KEGGiheo:C694_05235.
hpy:HP1011.
PATRICi20593357. VBIHelPyl33062_1059.

Phylogenomic databases

eggNOGiENOG4107QYT. Bacteria.
COG0167. LUCA.
KOiK00254.
OMAiERIKMGA.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00946.
BioCyciHPY:HP1011-MONOMER.

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_HELPY
AccessioniPrimary (citable) accession number: O25655
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: January 1, 1998
Last modified: October 5, 2016
This is version 117 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, Reference proteome

Documents

  1. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  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.