Reviewed, UniProtKB/Swiss-Prot Q53ZE5 (PYRDA_LACLC)

Names and origin

Protein names

Recommended name:
    Dihydroorotate dehydrogenase A
    EC=1.3.3.1
Alternative name(s):
    Dihydroorotate oxidase A
    DHOdehase A
      Short name=DHODase A
      Short name=DHOD A

Gene names

Name:

pyrDA

Organism

Lactococcus lactis subsp. cremoris (Streptococcus cremoris)

Taxonomic identifier

1359 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Lactobacillales › Streptococcaceae › Lactococcus

Protein attributes

Sequence length	311 AA.
Sequence status	Complete.
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; orotate from (S)-dihydroorotate (O2 route): step 1/1. HAMAP MF_00224
Subunit structure	Homodimer. HAMAP MF_00224
Subcellular location	Cytoplasm By similarity HAMAP MF_00224.
Miscellaneous	Can use fumarate but not NAD 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
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
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 311

311

Dihydroorotate dehydrogenase A HAMAP MF_00224

PRO_0000148394

Sites

Active site

130

1

Nucleophile HAMAP MF_00224

Experimental info

Mutagenesis

43

1

K → A: More than 500-fold reduction of enzymatic activity with oxygen or DCIP as electron acceptor. Ref.2

Mutagenesis

43

1

K → E: 40-fold reduction of enzymatic activity with oxygen as electron acceptor; more than 120-fold reduction with DCIP as electron acceptor. Ref.2

Mutagenesis

130

1

C → A: Almost total loss of activity with oxygen or DCIP as electron acceptor. Ref.2

Mutagenesis

130

1

C → S: Almost total loss of activity with oxygen or DCIP as electron acceptor. Ref.2

Mutagenesis

132

1

N → A: 54-fold reduction of enzymatic activity with oxygen as electron acceptor; more than 250-fold reduction with DCIP as electron acceptor. Ref.2

Mutagenesis

164

1

K → A: Almost total loss of activity with oxygen or DCIP as electron acceptor. Ref.2

Secondary structure

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311

Helix Strand Turn

Details...

Beta strand

4 – 6

3

Beta strand

9 – 17

9

Helix

26 – 34

9

Beta strand

58 – 61

4

Beta strand

64 – 67

4

Helix

76 – 89

14

Beta strand

92 – 94

3

Beta strand

97 – 100

4

Helix

105 – 117

13

Beta strand

122 – 128

7

Beta strand

133 – 135

3

Helix

139 – 141

3

Helix

143 – 153

11

Turn

154 – 156

3

Beta strand

161 – 165

5

Helix

171 – 181

11

Beta strand

188 – 191

4

Beta strand

195 – 199

5

Turn

203 – 206

4

Beta strand

207 – 209

3

Helix

212 – 215

4

Beta strand

216 – 221

6

Helix

222 – 224

3

Helix

225 – 236

12

Beta strand

243 – 250

8

Helix

254 – 263

10

Beta strand

266 – 270

5

Helix

272 – 277

6

Helix

281 – 296

16

Helix

301 – 303

3

Turn

304 – 306

3

Sequences

	Sequence		Length	Mass (Da)
	Q53ZE5-1 [UniParc]. Last modified May 24, 2005. Version 1. Checksum: 30157E3C2791CDD7	FASTA	311	34,210
	10 20 30 40 50 60 MLNTTFANAK FANPFMNASG VHCMTIEDLE ELKASQAGAY ITKSSTLEKR EGNPLPRYVD 70 80 90 100 110 120 LELGSINSMG LPNLGFDYYL DYVLKNQKEN AQEGPIFFSI AGMSAAENIA MLKKIQESDF 130 140 150 160 170 180 SGITELNLSC PNVPGKPQLA YDFEATEKLL KEVFTFFTKP LGVKLPPYFD LVHFDIMAEI 190 200 210 220 230 240 LNQFPLTYVN SVNSIGNGLF IDPEAESVVI KPKDGFGGIG GAYIKPTALA NVRAFYTRLK 250 260 270 280 290 300 PEIQIIGTGG IETGQDAFEH LLCGATMLQI GTALHKEGPA IFDRIIKELE EIMNQKGYQS 310 IADFHGKLKS L

References

[1]	"Lactococcus lactis subsp. cremoris gene encoding the biosynthetic enzyme dihydroorotate dehydrogenase family 1a." Hall C.R., Dietrich F.S. Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: NCK436.
[2]	"Active site of dihydroorotate dehydrogenase A from Lactococcus lactis investigated by chemical modification and mutagenesis." Bjoernberg O., Rowland P., Larsen S., Jensen K.F. Biochemistry 36:16197-16205(1997) [PubMed: 9405053] [Abstract] Cited for: MUTAGENESIS OF LYS-43; CYS-130; ASN-132 AND LYS-164.
[3]	"The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis." Rowland P., Nielsen F.S., Jensen K.F., Larsen S. Structure 5:239-252(1997) [PubMed: 9032071] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[4]	"The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function." Rowland P., Bjoernberg O., Nielsen F.S., Jensen K.F., Larsen S. Protein Sci. 7:1269-1279(1998) [PubMed: 9655329] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY323899 Genomic DNA. Translation: AAQ01776.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DOR	X-ray	2.00	A/B	1-311	[»]
1JQV	X-ray	2.10	A/B	1-311	[»]
1JQX	X-ray	1.70	A/B	1-311	[»]
1JRB	X-ray	1.90	A/B	1-311	[»]
1JRC	X-ray	1.80	A/B	1-311	[»]
1JUB	X-ray	1.40	A/B	1-311	[»]
1JUE	X-ray	1.80	A/B	1-311	[»]
1NFC	model	-	A	1-311	[»]
1OVD	X-ray	2.25	A/B	1-311	[»]
2BSL	X-ray	2.30	A/B	1-311	[»]
2BX7	X-ray	2.04	A/B	1-311	[»]
2DOR	X-ray	2.00	A/B	1-311	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

1.3.3.1. 289716.

Family and domain databases

HAMAP

MF_00224_B. DHO_dh_type1_B.
[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

PYRDA_LACLC

Accession

Primary (citable) accession number: Q53ZE5
Secondary accession number(s): P54321

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 2007
Last sequence update:	May 24, 2005
Last modified:	February 9, 2010
This is version 37 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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