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Protein

Dihydroorotate dehydrogenase (quinone)

Gene

pyrD

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
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

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).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 sitei71 – 711SubstrateUniRule annotation
Binding sitei91 – 911FMN; via amide nitrogenUniRule annotation
Binding sitei144 – 1441FMNUniRule annotation
Binding sitei177 – 1771FMNUniRule annotation
Binding sitei177 – 1771SubstrateUniRule annotation
Active sitei180 – 1801NucleophileUniRule annotation
Binding sitei182 – 1821SubstrateUniRule annotation
Binding sitei213 – 2131FMNUniRule annotation
Binding sitei241 – 2411FMN; via carbonyl oxygenUniRule annotation
Binding sitei265 – 2651FMN; via amide nitrogenUniRule annotation
Binding sitei294 – 2941FMN; via amide nitrogenUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi67 – 715FMNUniRule annotation
Nucleotide bindingi315 – 3162FMNUniRule 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

BioCyciMSME246196:GJ4Y-4197-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:MSMEG_4198, MSMEI_4100
OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Taxonomic identifieri246196 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacterium
Proteomesi
  • UP000006158 Componenti: Chromosome
  • UP000000757 Componenti: Chromosome

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 – 354354Dihydroorotate dehydrogenase (quinone)PRO_0000336475Add
BLAST

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

STRINGi246196.MSMEG_4198.

Structurei

3D structure databases

ProteinModelPortaliA0QZY9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni116 – 1205Substrate bindingUniRule annotation
Regioni242 – 2432Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

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

A0QZY9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMYRVLRRAL FLAPAERVHV WVFALLRAVT WAAPLRAALA RLLAPRDPIL
60 70 80 90 100
ASTVFGVHFP GPLGLAAGFD KNGRGLAAWG ALGFGYAEVG TVTAQPQPGN
110 120 130 140 150
PAPRLFRLPD DHALLNRMGF NNEGAGALAQ RLTRGKSDIP IGVNIGKTKV
160 170 180 190 200
TPAEEAVADY VTSARLLNSL ASFVVVNVSS PNTPGLRDLQ AVAALRPILA
210 220 230 240 250
AVKAETTKPV LVKIAPDLSD SDIDEIADLA VELGLAGIVA TNTTVSRDGL
260 270 280 290 300
LTPGVADLGP GGISGRPVAR RSAEVLRRLY RRVGDKLVLI SVGGIETADD
310 320 330 340 350
AWERIVSGAS LLQGYTGFIY GGGLWAKHIH DGIAGRLRAC GFTTLSEAVG

SAVR
Length:354
Mass (Da):37,167
Last modified:January 9, 2007 - v1
Checksum:i0B8D444388BC683A
GO

Sequence cautioni

The sequence AFP40558.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK69985.1.
CP001663 Genomic DNA. Translation: AFP40558.1. Different initiation.
RefSeqiWP_011729635.1. NC_008596.1.
YP_888477.1. NC_008596.1.

Genome annotation databases

EnsemblBacteriaiABK69985; ABK69985; MSMEG_4198.
AFP40558; AFP40558; MSMEI_4100.
GeneIDi4535978.
KEGGimsg:MSMEI_4100.
msm:MSMEG_4198.
PATRICi18080753. VBIMycSme59918_4119.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK69985.1.
CP001663 Genomic DNA. Translation: AFP40558.1. Different initiation.
RefSeqiWP_011729635.1. NC_008596.1.
YP_888477.1. NC_008596.1.

3D structure databases

ProteinModelPortaliA0QZY9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246196.MSMEG_4198.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK69985; ABK69985; MSMEG_4198.
AFP40558; AFP40558; MSMEI_4100.
GeneIDi4535978.
KEGGimsg:MSMEI_4100.
msm:MSMEG_4198.
PATRICi18080753. VBIMycSme59918_4119.

Phylogenomic databases

eggNOGiENOG4107QYT. Bacteria.
COG0167. LUCA.
HOGENOMiHOG000225103.
KOiK00254.
OMAiERIKMGA.
OrthoDBiEOG65BDN8.

Enzyme and pathway databases

UniPathwayiUPA00070; UER00946.
BioCyciMSME246196:GJ4Y-4197-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. Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C., Fraser C.M.
    Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  2. "Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?"
    Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C., Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.
    Genome Biol. 8:R20.1-R20.9(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.
  3. "Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol."
    Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M., Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.
    Genome Res. 19:128-135(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155.

Entry informationi

Entry nameiPYRD_MYCS2
AccessioniPrimary (citable) accession number: A0QZY9
Secondary accession number(s): I7FPB7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: January 9, 2007
Last modified: April 13, 2016
This is version 76 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.