P05020 (PYRC_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Dihydroorotase
Short name=DHOase
EC=3.5.2.3

Gene names

Name:	pyrC
Ordered Locus Names:	b1062, JW1049

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	348 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	(S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate. HAMAP-Rule MF_00219
Cofactor	Binds 2 zinc ions per subunit.
Pathway	Pyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 3/3. HAMAP-Rule MF_00219
Subunit structure	Homodimer.
Sequence similarities	Belongs to the DHOase family. Type 1 subfamily.

Ontologies

Keywords
Biological process	Pyrimidine biosynthesis
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	'de novo' UMP biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway 'de novo' pyrimidine nucleobase biosynthetic process Inferred from mutant phenotype PubMed 6370696. Source: EcoCyc
Molecular_function	dihydroorotase activity Inferred from direct assay PubMed 6142052. Source: EcoCyc zinc ion binding Inferred from direct assay PubMed 6142052. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.7

Chain

2 – 348

347

Dihydroorotase HAMAP-Rule MF_00219

PRO_0000147205

Sites

Metal binding

17

1

Zinc 1

Metal binding

19

1

Zinc 1

Metal binding

103

1

Zinc 1; via carbamate group

Metal binding

103

1

Zinc 2; via carbamate group

Metal binding

140

1

Zinc 2

Metal binding

178

1

Zinc 2

Metal binding

251

1

Zinc 1

Amino acid modifications

Modified residue

103

1

N6-carboxylysine HAMAP-Rule MF_00219

Secondary structure

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348

Helix Strand Turn

Details...

Beta strand

7 – 11

5

Beta strand

15 – 18

4

Helix

23 – 34

12

Beta strand

38 – 42

5

Helix

53 – 65

13

Beta strand

74 – 80

7

Helix

87 – 95

9

Beta strand

98 – 104

7

Turn

113 – 115

3

Helix

120 – 123

4

Helix

124 – 133

10

Beta strand

137 – 139

3

Helix

150 – 152

3

Helix

153 – 160

8

Helix

162 – 168

7

Turn

169 – 171

3

Beta strand

174 – 176

3

Helix

182 – 189

8

Beta strand

195 – 199

5

Helix

201 – 205

5

Helix

208 – 212

5

Helix

218 – 220

3

Helix

229 – 240

12

Beta strand

246 – 248

3

Helix

257 – 260

4

Beta strand

261 – 265

5

Turn

272 – 274

3

Helix

275 – 285

11

Helix

289 – 291

3

Helix

292 – 297

6

Helix

299 – 304

6

Beta strand

312 – 316

5

Beta strand

329 – 333

5

Turn

336 – 339

4

Beta strand

341 – 343

3

Sequences

	Sequence		Length	Mass (Da)
	P05020 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 179B35324204A111	FASTA	348	38,827
	10 20 30 40 50 60 MTAPSQVLKI RRPDDWHLHL RDGDMLKTVV PYTSEIYGRA IVMPNLAPPV TTVEAAVAYR 70 80 90 100 110 120 QRILDAVPAG HDFTPLMTCY LTDSLDPNEL ERGFNEGVFT AAKLYPANAT TNSSHGVTSI 130 140 150 160 170 180 DAIMPVLERM EKIGMPLLVH GEVTHADIDI FDREARFIES VMEPLRQRLT ALKVVFEHIT 190 200 210 220 230 240 TKDAADYVRD GNERLAATIT PQHLMFNRNH MLVGGVRPHL YCLPILKRNI HQQALRELVA 250 260 270 280 290 300 SGFNRVFLGT DSAPHARHRK ESSCGCAGCF NAPTALGSYA TVFEEMNALQ HFEAFCSVNG 310 320 330 340 PQFYGLPVND TFIELVREEQ QVAESIALTD DTLVPFLAGE TVRWSVKQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the structural gene for dihydroorotase of Escherichia coli K12." Baeckstroem D., Sjoeberg R.-M., Lundberg L.G. Eur. J. Biochem. 160:77-82(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Nucleotide sequence and expression of the pyrC gene of Escherichia coli K-12." Wilson H.R., Chan P.T., Turnbough C.L. Jr. J. Bacteriol. 169:3051-3058(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	Ohmori H. Submitted (MAY-1994) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 86-348. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13. Strain: K12 / EMG2.
[8]	"Dihydroorotase from Escherichia coli. Substitution of Co(II) for the active site Zn(II)." Brown D.C., Collins K.D. J. Biol. Chem. 266:1597-1604(1991) [PubMed] [Europe PMC] [Abstract] Cited for: ZINC-BINDING.
[9]	"Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center." Thoden J.B., Phillips G.N. Jr., Neal T.M., Raushel F.M., Holden H.M. Biochemistry 40:6989-6997(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS), CARBAMYLATION AT LYS-103.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X04469 Genomic DNA. Translation: CAA28157.1.
M16752 Genomic DNA. Translation: AAA24482.1.
U00096 Genomic DNA. Translation: AAC74146.1.
AP009048 Genomic DNA. Translation: BAA35870.1.
D31709 Genomic DNA. Translation: BAA06514.1.

PIR

DEECOO. A25008.

RefSeq

NP_415580.1. NC_000913.2.
YP_489330.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1J79	X-ray	1.70	A/B	2-348	[»]
1XGE	X-ray	1.90	A/B	2-347	[»]
2E25	X-ray	2.70	A	2-347	[»]
2EG6	X-ray	1.70	A/B	2-348	[»]
2EG7	X-ray	2.00	A/B	2-348	[»]
2EG8	X-ray	2.20	A/B	2-348	[»]
2Z24	X-ray	1.90	A/B	2-348	[»]
2Z25	X-ray	1.87	A/B	2-348	[»]
2Z26	X-ray	1.29	A/B	2-348	[»]
2Z27	X-ray	1.87	A/B	2-348	[»]
2Z28	X-ray	1.87	A/B	2-348	[»]
2Z29	X-ray	1.90	A/B	2-348	[»]
2Z2A	X-ray	1.87	A/B	2-348	[»]
2Z2B	X-ray	1.85	A	2-348	[»]

ProteinModelPortal

P05020.

SMR

P05020. Positions 4-347.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10624N.

IntAct

P05020. 2 interactions.

STRING

511145.b1062.

Protein family/group databases

MEROPS

M38.A02.

Proteomic databases

PaxDb

P05020.

PRIDE

P05020.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74146; AAC74146; b1062.
BAA35870; BAA35870; BAA35870.

GeneID

12932767.
945787.

KEGG

ecj:Y75_p1032.
eco:b1062.

PATRIC

32117363. VBIEscCol129921_1104.

Organism-specific databases

EchoBASE

EB0799.

EcoGene

EG10806. pyrC.

Phylogenomic databases

eggNOG

COG0418.

HOGENOM

HOG000256259.

KO

K01465.

OMA

FEHITTE.

ProtClustDB

PRK05451.

Enzyme and pathway databases

BioCyc

EcoCyc:DIHYDROOROT-MONOMER.
ECOL316407:JW1049-MONOMER.
MetaCyc:DIHYDROOROT-MONOMER.

BRENDA

3.5.2.3. 2026.

SABIO-RK

P05020.

UniPathway

UPA00070; UER00117.

Gene expression databases

Genevestigator

P05020.

Family and domain databases

HAMAP

MF_00219. PyrC_type1.

InterPro

IPR006680. Amidohydro_1.
IPR004721. DHOdimr.
IPR002195. Dihydroorotase_CS.
[Graphical view]

Pfam

PF01979. Amidohydro_1. 1 hit.
[Graphical view]

PIRSF

PIRSF001237. DHOdimr. 1 hit.

TIGRFAMs

TIGR00856. pyrC_dimer. 1 hit.

PROSITE

PS00482. DIHYDROOROTASE_1. 1 hit.
PS00483. DIHYDROOROTASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P05020.

EvolutionaryTrace

P05020.

Entry information

Entry name

PYRC_ECOLI

Accession

Primary (citable) accession number: P05020

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 131 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program