P0A7E1 (PYRD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Dihydroorotate dehydrogenase (quinone)
EC=1.3.5.2

Alternative name(s):
DHOdehase
Short name=DHOD
Short name=DHODase
Dihydroorotate oxidase

Gene names

Name:	pyrD
Ordered Locus Names:	b0945, JW0928

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	336 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor. Ref.5
Catalytic activity	(S)-dihydroorotate + a quinone = orotate + a quinol. Ref.5
Cofactor	Binds 1 FMN per subunit. Ref.6
Pathway	Pyrimidine metabolism; UMP biosynthesis via de novo pathway; orotate from (S)-dihydroorotate (quinone route): step 1/1. HAMAP MF_00225
Subunit structure	Monomer. Ref.6
Subcellular location	Cell membrane; Peripheral membrane protein HAMAP MF_00225.
Sequence similarities	Belongs to the dihydroorotate dehydrogenase family. Type 2 subfamily.
Biophysicochemical properties	Kinetic parameters: KM=28.8 µM for dihydroorotate Ref.5 Vmax=180 µmol/min/mg enzyme

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Cellular component	Cell membrane Membrane
Ligand	FMN Flavoprotein
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	'de novo' pyrimidine base biosynthetic process Inferred from mutant phenotype. Source: EcoCyc UMP biosynthetic process Inferred from electronic annotation. Source: InterPro
Cellular component	plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	FMN binding Inferred from direct assay Ref.1. Source: EcoCyc dihydroorotate oxidase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 336

336

Dihydroorotate dehydrogenase (quinone) HAMAP MF_00225

PRO_0000148437

Regions

Nucleotide binding

62 – 66

5

FMN HAMAP MF_00225

Nucleotide binding

318 – 319

2

FMN HAMAP MF_00225

Region

111 – 115

5

Substrate binding HAMAP MF_00225

Region

246 – 247

2

Substrate binding HAMAP MF_00225

Sites

Active site

175

1

Nucleophile

Binding site

66

1

Substrate

Binding site

86

1

FMN; via amide nitrogen

Binding site

139

1

FMN

Binding site

172

1

FMN

Binding site

172

1

Substrate

Binding site

177

1

Substrate

Binding site

217

1

FMN

Binding site

245

1

FMN; via carbonyl oxygen

Binding site

268

1

FMN; via amide nitrogen

Binding site

297

1

FMN; via amide nitrogen

Experimental info

Mutagenesis

175

1

S → A: Almost no activity. Ref.5

Mutagenesis

175

1

S → C: 500-fold reduction in activity. Ref.5

Secondary structure

1

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336

Helix Strand Turn

Details...

Helix

3 – 10

8

Helix

15 – 29

15

Helix

33 – 37

5

Beta strand

47 – 49

3

Beta strand

52 – 60

9

Helix

71 – 76

6

Beta strand

80 – 87

8

Beta strand

100 – 103

4

Turn

104 – 107

4

Beta strand

108 – 111

4

Helix

120 – 129

10

Beta strand

134 – 140

7

Helix

148 – 151

4

Helix

152 – 162

11

Helix

163 – 165

3

Beta strand

167 – 172

6

Beta strand

176 – 178

3

Helix

181 – 185

5

Helix

187 – 208

22

Beta strand

214 – 217

4

Helix

224 – 236

13

Beta strand

240 – 244

5

Turn

258 – 261

4

Beta strand

263 – 268

6

Helix

269 – 271

3

Helix

272 – 286

15

Beta strand

292 – 297

6

Helix

301 – 310

10

Beta strand

313 – 318

6

Helix

319 – 324

6

Helix

326 – 335

10

Sequences

	Sequence		Length	Mass (Da)
	P0A7E1 [UniParc]. Last modified August 13, 1987. Version 1. Checksum: 973227EAE6B83622	FASTA	336	36,775
	10 20 30 40 50 60 MYYPFVRKAL FQLDPERAHE FTFQQLRRIT GTPFEALVRQ KVPAKPVNCM GLTFKNPLGL 70 80 90 100 110 120 AAGLDKDGEC IDALGAMGFG SIEIGTVTPR PQPGNDKPRL FRLVDAEGLI NRMGFNNLGV 130 140 150 160 170 180 DNLVENVKKA HYDGVLGINI GKNKDTPVEQ GKDDYLICME KIYAYAGYIA INISSPNTPG 190 200 210 220 230 240 LRTLQYGEAL DDLLTAIKNK QNDLQAMHHK YVPIAVKIAP DLSEEELIQV ADSLVRHNID 250 260 270 280 290 300 GVIATNTTLD RSLVQGMKNC DQTGGLSGRP LQLKSTEIIR RLSLELNGRL PIIGVGGIDS 310 320 330 VIAAREKIAA GASLVQIYSG FIFKGPPLIK EIVTHI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the pyrD gene of Escherichia coli and characterization of the flavoprotein dihydroorotate dehydrogenase." Larsen N.J., Jensen K.F. Eur. J. Biochem. 151:59-65(1985) [PubMed: 2992959] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-7.
[2]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed: 8905232] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis." Bjoernberg O., Gruener A.-C., Roepstorff P., Jensen K.F. Biochemistry 38:2899-2908(1999) [PubMed: 10074342] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-10 AND 183-192, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF SER-175, ENZYME KINETICS.
[6]	"E. coli dihydroorotate dehydrogenase reveals structural and functional distinctions between different classes of dihydroorotate dehydrogenases." Noerager S., Jensen K.F., Bjoernberg O., Larsen S. Structure 10:1211-1223(2002) [PubMed: 12220493] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH FMN AND OROTATE, COFACTOR, SUBUNIT, REACTION MECHANISM.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X02826 Genomic DNA. Translation: CAA26594.1.
U00096 Genomic DNA. Translation: AAC74031.1.
AP009048 Genomic DNA. Translation: BAA35700.1.

PIR

DEECDO. A23109.

RefSeq

NP_415465.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1F76	X-ray	2.50	A/B/D/E	1-336	[»]

ProteinModelPortal

P0A7E1.

SMR

P0A7E1. Positions 1-336.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35945N.

IntAct

P0A7E1. 6 interactions.

2D gel databases

SWISS-2DPAGE

P0A7E1.

Proteomic databases

PRIDE

P0A7E1.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000005052; EBESCP00000005052; EBESCG00000004123.
EBESCT00000014954; EBESCP00000014245; EBESCG00000014014.

GeneID

945556.

GenomeReviews

Gene locus JW0928 in contig AP009048_GR.
Gene locus b0945 in contig U00096_GR.

KEGG

ecj:JW0928.
eco:b0945.

PATRIC

32117109. VBIEscCol129921_0979.

Organism-specific databases

EchoBASE

EB0800.

EcoGene

EG10807. pyrD.

Phylogenomic databases

eggNOG

COG0167.

GeneTree

EBGT00050000011106.

HOGENOM

HBG351027.

OMA

SYVTVNI.

PhylomeDB

P0A7E1.

ProtClustDB

PRK05286.

Enzyme and pathway databases

BioCyc

EcoCyc:DIHYDROOROTOX-MONOMER.
MetaCyc:DIHYDROOROTOX-MONOMER.

Gene expression databases

Genevestigator

P0A7E1.

Family and domain databases

HAMAP

MF_00225. DHO_dh_type2.
[Tree]

InterPro

IPR013785. Aldolase_TIM.
IPR012135. Dihydroorotate_DH_1_2.
IPR005719. Dihydroorotate_DH_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

TIGR01036. PyrD_sub2. 1 hit.

PROSITE

PS00911. DHODEHASE_1. 1 hit.
PS00912. DHODEHASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

PYRD_ECOLI

Accession

Primary (citable) accession number: P0A7E1
Secondary accession number(s): P05021

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	August 13, 1987
Last modified:	January 25, 2012
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program