Q7MVJ6 (PYRDB_PORGI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit
Short name=DHOD B
Short name=DHODase B
Short name=DHOdehase B
EC=1.3.1.14

Alternative name(s):
Dihydrdoorotate oxidase B
Orotate reductase (NADH)

Gene names

Name:	pyrD
Ordered Locus Names:	PG_1065

Organism

Porphyromonas gingivalis (strain ATCC BAA-308 / W83) [Complete proteome] [HAMAP]

Taxonomic identifier

242619 [NCBI]

Taxonomic lineage

Bacteria › Bacteroidetes › Bacteroidia › Bacteroidales › Porphyromonadaceae › Porphyromonas

Protein attributes

Sequence length	307 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the conversion of dihydroorotate to orotate with NAD+ as electron acceptor By similarity. HAMAP MF_00224
Catalytic activity	(S)-dihydroorotate + NAD+ = orotate + NADH. HAMAP MF_00224
Cofactor	Binds 1 FMN per subunit By similarity. HAMAP MF_00224
Pathway	Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (NAD(+) route): step 1/1. HAMAP MF_00224
Subunit structure	Heterotetramer of 2 PyrK and 2 PyrD type B subunits By similarity.
Subcellular location	Cytoplasm By similarity HAMAP MF_00224.
Sequence similarities	Belongs to the dihydroorotate dehydrogenase family. Type 1 subfamily.

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Cellular component	Cytoplasm
Ligand	FMN Flavoprotein NAD
Molecular function	Oxidoreductase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	'de novo' pyrimidine base biosynthetic process Inferred from electronic annotation. Source: InterPro UMP biosynthetic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	dihydroorotate oxidase activity Inferred from electronic annotation. Source: InterPro orotate reductase (NADH) activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 307	307	Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit HAMAP MF_00224		PRO_1000100225
Regions
	Nucleotide binding	46 – 47	2	FMN By similarity
	Nucleotide binding	244 – 245	2	FMN By similarity
	Region	70 – 74	5	Substrate binding By similarity
	Region	193 – 194	2	Substrate binding By similarity
Sites
	Active site	131	1	Nucleophile
	Binding site	22	1	FMN By similarity
	Binding site	46	1	Substrate By similarity
	Binding site	100	1	FMN By similarity
	Binding site	128	1	FMN By similarity
	Binding site	128	1	Substrate By similarity
	Binding site	166	1	FMN By similarity
	Binding site	192	1	FMN; via carbonyl oxygen By similarity
	Binding site	218	1	FMN; via amide nitrogen By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q7MVJ6 [UniParc]. Last modified December 15, 2003. Version 1. Checksum: DCDE728C6AA8A218	FASTA	307	33,120
	10 20 30 40 50 60 MVRTEVEIGR GLTIKNPVMT ASGTYGYGTE YKDFIDIDRL GAIVVKGTTL HHREGNAYPR 70 80 90 100 110 120 MAETPSGMLN AVGLQNKGVH YFVEHIYPVI KDYRTEMIVN VSGSTLDDYA ETSRIINELE 130 140 150 160 170 180 HIRAIELNIS CPNVKQGGMA YGVTCEGAAS VVKAVRRAYD KTLIVKLSPN VTDITEIARA 190 200 210 220 230 240 VESEGADAIS MVNTFLGMAI DAEKRRPILS TTTGGLSGPC IKPIALRMVW QTAKVVQVPI 250 260 270 280 290 300 IGMGGIASAA DAIEFLLAGA TAVQVGCYNF VDPAAASYIV DGIEDYLRRH GISDVKELIG SLVIEHN

References

[1]

"Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83." Nelson K.E., Fleischmann R.D., DeBoy R.T., Paulsen I.T., Fouts D.E., Eisen J.A., Daugherty S.C., Dodson R.J., Durkin A.S., Gwinn M.L., Haft D.H., Kolonay J.F., Nelson W.C., Mason T.M., Tallon L., Gray J., Granger D., Tettelin H. , Dong H., Galvin J.L., Duncan M.J., Dewhirst F.E., Fraser C.M. J. Bacteriol. 185:5591-5601(2003) [PubMed: 12949112] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-308 / W83.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE015924 Genomic DNA. Translation: AAQ66179.1.
RefSeq	NP_905280.1. NC_002950.2.
3D structure databases
HSSP	HSSP built from PDB template 1EP3 based on UniProtKB P54322.
ProteinModelPortal	Q7MVJ6.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	2553121.
GenomeReviews	Gene locus PG_1065 in contig AE015924_GR.
KEGG	pgi:PG1065.
NMPDR	fig|242619.1.peg.921.
PATRIC	22979174. VBIPorGin134034_0982.
TIGR	PG_1065.
Phylogenomic databases
HOGENOM	HBG472415.
OMA	VALRMVW.
PhylomeDB	Q7MVJ6.
ProtClustDB	PRK07259.
Enzyme and pathway databases
BioCyc	PGIN242619:PG_1065-MONOMER.
Family and domain databases
HAMAP	MF_00224. DHO_dh_type1. [Tree]
InterPro	IPR013785. Aldolase_TIM. IPR005720. Dihydroorotate_DH. IPR024920. Dihydroorotate_DH_1. IPR012135. Dihydroorotate_DH_1_2. IPR001295. Dihydroorotate_DH_CS. [Graphical view]
Gene3D	G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.
KO	K00226.
Pfam	PF01180. DHO_dh. 1 hit. [Graphical view]
PIRSF	PIRSF000164. DHO_oxidase. 1 hit.
TIGRFAMs	TIGR01037. PyrD_sub1_fam. 1 hit.
PROSITE	PS00911. DHODEHASE_1. 1 hit. PS00912. DHODEHASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PYRDB_PORGI

Accession

Primary (citable) accession number: Q7MVJ6

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 24, 2009
Last sequence update:	December 15, 2003
Last modified:	January 25, 2012
This is version 66 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program