Reviewed, UniProtKB/Swiss-Prot P54322 (PYRDB_LACLM)

Names and origin

Protein names

Recommended name:
    Dihydroorotate dehydrogenase B, catalytic subunit
    EC=1.3.3.1
Alternative name(s):
    Dihydroorotate oxidase B
    DHOdehase B
      Short name=DHODase B
      Short name=DHOD B

Gene names

Name:	pyrDB
Ordered Locus Names:	llmg_1106

Organism

Lactococcus lactis subsp. cremoris (strain MG1363) [Complete proteome] [HAMAP]

Taxonomic identifier

416870 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Lactobacillales › Streptococcaceae › Lactococcus

Protein attributes

Sequence length	311 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	(S)-dihydroorotate + O2 = orotate + H2O2. HAMAP MF_00224
Cofactor	Binds 1 FMN per subunit. HAMAP MF_00224
Pathway	Pyrimidine metabolism; UMP biosynthesis via de novo pathway; UMP from HCO(3)(-): step 4/6. HAMAP MF_00224
Subunit structure	Heterotetramer of 2 pyrK and 2 pyrDB subunits. HAMAP MF_00224
Subcellular location	Cytoplasm. HAMAP MF_00224
Miscellaneous	Can use NAD but not fumarate as an electron acceptor. 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
Molecular function	Oxidoreductase
Technical term	3D-structure 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 oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	dihydroorotate oxidase activity Inferred from electronic annotation. Source: HAMAP protein binding Ref.5 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
pyrK	P56968	1	EBI-1030598,EBI-1030589

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 311

311

Dihydroorotate dehydrogenase B, catalytic subunit HAMAP MF_00224

PRO_0000148396

Sites

Active site

135

1

Nucleophile HAMAP MF_00224

Experimental info

Sequence conflict

123

1

A → R in CAA52280. Ref.1

Sequence conflict

123

1

A → R Ref.2

Sequence conflict

239

1

V → D in CAA52280. Ref.1

Sequence conflict

239

1

V → D Ref.2

Sequence conflict

255

1

D → V in CAA52280. Ref.1

Sequence conflict

255

1

D → V Ref.2

Sequence conflict

266

1

A → R in CAA52280. Ref.1

Sequence conflict

266

1

A → R Ref.2

Secondary structure

1

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311

Helix Strand Turn

Details...

Helix

5 – 7

3

Beta strand

9 – 11

3

Beta strand

14 – 22

9

Helix

31 – 34

4

Helix

39 – 41

3

Beta strand

45 – 50

6

Beta strand

63 – 66

4

Beta strand

69 – 72

4

Helix

81 – 86

6

Helix

88 – 95

8

Beta strand

101 – 105

5

Helix

110 – 120

11

Beta strand

126 – 132

7

Beta strand

135 – 137

3

Turn

138 – 142

5

Helix

145 – 147

3

Helix

149 – 162

14

Beta strand

167 – 170

4

Helix

179 – 187

9

Beta strand

191 – 195

5

Beta strand

199 – 201

3

Turn

206 – 209

4

Beta strand

210 – 213

4

Beta strand

218 – 222

5

Helix

223 – 225

3

Helix

226 – 237

12

Beta strand

244 – 246

3

Helix

253 – 262

10

Beta strand

265 – 269

5

Helix

272 – 275

4

Helix

279 – 293

15

Helix

299 – 308

10

Sequences

	Sequence		Length	Mass (Da)
	P54322-1 [UniParc]. Last modified May 1, 2007. Version 2. Checksum: 1854517E5B585BB9	FASTA	311	32,930
	10 20 30 40 50 60 MTENNRLSVK LPGLDLKNPI IPASGCFGFG EEYAKYYDLN KLGSIMVKAT TLHPRFGNPT 70 80 90 100 110 120 PRVAETASGM LNAIGLQNPG LEVIMTEKLP WLNENFPELP IIANVAGSEE ADYVAVCAKI 130 140 150 160 170 180 GDAANVKAIE LNISCPNVKH GGQAFGTDPE VAAALVKACK AVSKVPLYVK LSPNVTDIVP 190 200 210 220 230 240 IAKAVEAAGA DGLTMINTLM GVRFDLKTRQ PILANITGGL SGPAIKPVAL KLIHQVAQVV 250 260 270 280 290 300 DIPIIGMGGV ANAQDVLEMY MAGASAVAVG TANFADPFVC PKIIDKLPEL MDQYRIESLE 310 SLIQEVKEGK K

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Two different dihydroorotate dehydrogenases in Lactococcus lactis." Andersen P.S., Jansen P.J.G., Hammer K. J. Bacteriol. 176:3975-3982(1994) [PubMed: 8021180] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Sequence analysis and identification of the pyrKDbF operon from Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine biosynthesis." Andersen P.S., Martinussen J., Hammer K. J. Bacteriol. 178:5005-5012(1996) [PubMed: 8759867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The complete genome sequence of the lactic acid bacterial paradigm Lactococcus lactis subsp. cremoris MG1363." Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C., Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P., van Sinderen D., Kok J. J. Bacteriol. 189:3256-3270(2007) [PubMed: 17307855] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"The B form of dihydroorotate dehydrogenase from Lactococcus lactis consists of two different subunits, encoded by the pyrDb and pyrK genes, and contains FMN, FAD, and [FeS] redox centers." Nielsen F.S., Andersen P.S., Jensen K.F. J. Biol. Chem. 271:29359-29365(1996) [PubMed: 8910599] [Abstract] Cited for: CHARACTERIZATION.
[5]	"Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster." Rowland P., Noerager S., Jensen K.F., Larsen S. Structure 8:1227-1238(2000) [PubMed: 11188687] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

Cross-references

Sequence databases

EMBLGenBankDDBJ

X74207 Genomic DNA. Translation: CAA52280.1.
AM406671 Genomic DNA. Translation: CAL97700.1.

RefSeq

YP_001032420.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EP1	X-ray	2.20	A	1-311	[»]
1EP2	X-ray	2.40	A	1-311	[»]
1EP3	X-ray	2.10	A	1-311	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P54322. 1 interaction.

Genome annotation databases

GeneID

4798332.

GenomeReviews

Gene locus llmg_1106 in contig AM406671_GR.

KEGG

llm:llmg_1106.

Organism-specific databases

CMR

Search...

Phylogenomic databases

OMA

P54322. NSIGLQN.

Family and domain databases

HAMAP

MF_00224.
[Tree]

InterPro

IPR013785. Aldolase_TIM.
IPR012135. Dihydroorotate_DH_1_2.
IPR005720. Dihydroorotate_DH_1_core.
IPR001295. Dihydroorotate_DH_CS.
[Graphical view]

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.

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_LACLM

Accession

Primary (citable) accession number: P54322
Secondary accession number(s): A2RK90

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	May 1, 2007
Last modified:	June 16, 2009
This is version 69 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)