O59185 (PYRDB_PYRHO) 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:	PH1516

Organism

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) [Complete proteome] [HAMAP]

Taxonomic identifier

70601 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	303 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 – 303	303	Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit HAMAP MF_00224		PRO_0000148414
Regions
	Nucleotide binding	47 – 48	2	FMN By similarity
	Nucleotide binding	241 – 242	2	FMN By similarity
	Nucleotide binding	263 – 264	2	FMN By similarity
	Region	71 – 75	5	Substrate binding By similarity
	Region	190 – 191	2	Substrate binding By similarity
Sites
	Active site	128	1	Nucleophile
	Binding site	23	1	FMN By similarity
	Binding site	47	1	Substrate By similarity
	Binding site	125	1	FMN By similarity
	Binding site	125	1	Substrate By similarity
	Binding site	163	1	FMN By similarity
	Binding site	189	1	FMN; via carbonyl oxygen By similarity
	Binding site	215	1	FMN; via amide nitrogen By similarity

Sequences

	Sequence		Length	Mass (Da)
	O59185 [UniParc]. Last modified August 1, 1998. Version 1. Checksum: 16385BF30E51A226	FASTA	303	32,700
	10 20 30 40 50 60 MVKRMLEVKL FGIRFENPLI LASGVVDMTP ELLRRAHNEG AGGVVTKSIG KEPRKGYDNP 70 80 90 100 110 120 TIVELPYGLI NAMGLPNPGW EAFLNEFIDE RFDFPVIVSI FGGTPEEFAF LAEKLEPVAD 130 140 150 160 170 180 AFELNLSCPH AKGYGMEIGQ DPKNVYEVVK AVKDVTDKPV IAKLTPNVND ITKLGLAAER 190 200 210 220 230 240 GGADGVSAIN TVKAIAIDIY AKRPILSNKV GGYSGPGIKP IALRAVYDLA KVLDIPVIGI 250 260 270 280 290 300 GGITSWRDAV EFLLAGASAL QIGTAVYLRG FKVFKEISNG IIEYLKEEGF SSIRDIIGLA LKV

References

[1]

"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3." Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T. , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H. DNA Res. 5:55-76(1998) [PubMed: 9679194] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000001 Genomic DNA. Translation: BAA30624.1.
PIR	H71027.
RefSeq	NP_143376.1. NC_000961.1.
3D structure databases
ProteinModelPortal	O59185.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	EBPYRT00000000128; EBPYRP00000000128; EBPYRG00000000128.
GeneID	1443832.
GenomeReviews	Gene locus PH1516 in contig BA000001_GR.
KEGG	pho:PH1516.
NMPDR	fig|70601.1.peg.1485.
Organism-specific databases
CMR	Search...
Phylogenomic databases
GeneTree	EBGT00050000023023.
HOGENOM	HBG472415.
OMA	HAKGYGM.
PhylomeDB	O59185.
ProtClustDB	PRK07259.
Enzyme and pathway databases
BioCyc	PHOR70601:PH1516-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_PYRHO

Accession

Primary (citable) accession number: O59185

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 2000
Last sequence update:	August 1, 1998
Last modified:	January 25, 2012
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program