P26297 (LDHD_LACDA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-lactate dehydrogenase
Short name=D-LDH
EC=1.1.1.28

Alternative name(s):
D-specific D-2-hydroxyacid dehydrogenase

Gene names

Name:	ldhA
Ordered Locus Names:	Ldb0101

Organism

Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081) [Complete proteome] [HAMAP]

Taxonomic identifier

390333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Lactobacillales › Lactobacillaceae › Lactobacillus › Lactobacillus delbrueckii › Lactobacillus delbrueckii subsp. bulgaricus

Protein attributes

Sequence length	333 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	(R)-lactate + NAD+ = pyruvate + NADH.
Subunit structure	Homodimer. Ref.8
Sequence similarities	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.

Ontologies

Keywords
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Molecular_function	D-lactate dehydrogenase activity Inferred from electronic annotation. Source: EC NAD binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed

Chain

2 – 333

332

D-lactate dehydrogenase

PRO_0000075953

Regions

Nucleotide binding

153 – 179

27

NADH

Nucleotide binding

156 – 157

2

NAD By similarity

Nucleotide binding

234 – 236

3

NAD By similarity

Nucleotide binding

297 – 300

4

NAD By similarity

Sites

Active site

236

1

Active site

265

1

Active site

297

1

Proton donor

Binding site

260

1

NAD By similarity

Experimental info

Mutagenesis

206

1

H → Q: Increase of activity. Ref.6

Mutagenesis

236

1

R → K: Decrease of activity. Ref.6

Mutagenesis

260

1

D → N: Decrease of activity. Ref.6

Mutagenesis

265

1

E → Q: Decrease of activity. Ref.6

Mutagenesis

297

1

H → Q: 90% loss of activity. Ref.6

Sequence conflict

41

1

V → A in AAA25246. Ref.2

Sequence conflict

117

1

R → A in CAA42781. Ref.1

Sequence conflict

122

1

D → A in AAA25246. Ref.2

Sequence conflict

152

1

I → V in AAA25246. Ref.2

Sequence conflict

174

1

A → T in CAA42781. Ref.1

Sequence conflict

220

1

E → K in AAA25246. Ref.2

Sequence conflict

254

1

I → V in AAA25246. Ref.2

Sequence conflict

268

1

I → V in AAA25246. Ref.2

Sequence conflict

273

1

W → R in AAA25246. Ref.2

Secondary structure

1

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333

Helix Strand Turn

Details...

Beta strand

3 – 6

4

Helix

11 – 13

3

Helix

14 – 22

9

Beta strand

27 – 31

5

Turn

38 – 40

3

Helix

41 – 44

4

Beta strand

48 – 52

5

Helix

60 – 68

9

Beta strand

73 – 79

7

Helix

86 – 91

6

Beta strand

95 – 97

3

Helix

104 – 120

17

Helix

122 – 130

9

Helix

144 – 146

3

Beta strand

147 – 152

6

Helix

156 – 167

12

Beta strand

171 – 175

5

Helix

181 – 185

5

Helix

193 – 199

7

Beta strand

201 – 205

5

Helix

211 – 213

3

Helix

219 – 224

6

Beta strand

229 – 233

5

Helix

237 – 239

3

Helix

242 – 250

9

Beta strand

253 – 260

8

Turn

266 – 270

5

Helix

281 – 288

8

Beta strand

292 – 294

3

Helix

303 – 321

19

Beta strand

327 – 329

3

Sequences

	Sequence		Length	Mass (Da)
	P26297 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 16E8B68D54B9D9D4	FASTA	333	37,049
	10 20 30 40 50 60 MTKIFAYAIR EDEKPFLKEW EDAHKDVEVE YTDKLLTPET VALAKGADGV VVYQQLDYTA 70 80 90 100 110 120 ETLQALADNG ITKMSLRNVG VDNIDMAKAK ELGFQITNVP VYSPNAIAEH AAIQAARILR 130 140 150 160 170 180 QDKAMDEKVA RHDLRWAPTI GREVRDQVVG VIGTGHIGQV FMQIMEGFGA KVIAYDIFRN 190 200 210 220 230 240 PELEKKGYYV DSLDDLYKQA DVISLHVPDV PANVHMINDE SIAKMKQDVV IVNVSRGPLV 250 260 270 280 290 300 DTDAVIRGLD SGKIFGYAMD VYEGEVGIFN EDWEGKEFPD ARLADLIARP NVLVTPHTAF 310 320 330 YTTHAVRNMV VKAFDNNLEL VEGKEAETPV KVG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning of the D-lactate dehydrogenase gene from Lactobacillus delbrueckii subsp. bulgaricus by complementation in Escherichia coli." Bernard N., Ferain T., Garmyn D., Hols P., Delcour J. FEBS Lett. 290:61-64(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Primary structure, physicochemical properties, and chemical modification of NAD(+)-dependent D-lactate dehydrogenase. Evidence for the presence of Arg-235, His-303, Tyr-101, and Trp-19 at or near the active site." Kochhar S., Hunziker P., Leong-Morgenthaler P.M., Hottinger H. J. Biol. Chem. 267:8499-8513(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
[3]	"Cloning and overexpression of the Lactobacillus bulgaricus NAD(+)-dependent D-lactate dehydrogenase gene in Escherichia coli: purification and characterization of the recombinant enzyme." Kochhar S., Chuard N., Hottinger H. Biochem. Biophys. Res. Commun. 185:705-712(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution." van de Guchte M., Penaud S., Grimaldi C., Barbe V., Bryson K., Nicolas P., Robert C., Oztas S., Mangenot S., Couloux A., Loux V., Dervyn R., Bossy R., Bolotin A., Batto J.-M., Walunas T., Gibrat J.-F., Bessieres P. , Weissenbach J., Ehrlich S.D., Maguin E. Proc. Natl. Acad. Sci. U.S.A. 103:9274-9279(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 11842 / DSM 20081.
[5]	"Evolutionary relationship of NAD(+)-dependent D-lactate dehydrogenase: comparison of primary structure of 2-hydroxy acid dehydrogenases." Kochhar S., Hunziker P., Leong-Morgenthaler P.M., Hottinger H. Biochem. Biophys. Res. Commun. 184:60-66(1992) [PubMed] [Europe PMC] [Abstract] Cited for: SIMILARITY TO OTHER ENZYMES OF THIS FAMILY.
[6]	"D-2-hydroxy-4-methylvalerate dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus. II. Mutagenic analysis of catalytically important residues." Bernard N., Johnsen K., Gelpi J.L., Alvarez J.A., Ferain T., Garmyn D., Hols P., Cortes A., Clarke A.R., Holbrook J.J., Delcour J. Eur. J. Biochem. 244:213-219(1997) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF HIS-206; ARG-236; ASP-260; GLU-265 AND HIS-297.
[7]	"Prediction of structurally conserved regions of D-specific hydroxy acid dehydrogenases by multiple alignment with formate dehydrogenase." Vinals C., Depiereux E., Feytmans E. Biochem. Biophys. Res. Commun. 192:182-188(1993) [PubMed] [Europe PMC] [Abstract] Cited for: 3D-STRUCTURE MODELING.
[8]	"Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus." Razeto A., Kochhar S., Hottinger H., Dauter M., Wilson K.S., Lamzin V.S. J. Mol. Biol. 318:109-119(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH NADH, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X60220 Genomic DNA. Translation: CAA42781.1.
M85224 Genomic DNA. Translation: AAA25246.1.
CR954253 Genomic DNA. Translation: CAI96942.1.

PIR

A38094.

RefSeq

YP_618304.1. NC_008054.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DLD	model	-	A	1-333	[»]
1J49	X-ray	2.20	A/B	1-333	[»]
1J4A	X-ray	1.90	A/B/C/D	1-333	[»]

ProteinModelPortal

P26297.

SMR

P26297. Positions 1-332.

ModBase

Search...

Protein-protein interaction databases

STRING

390333.Ldb0101.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAI96942; CAI96942; Ldb0101.

GeneID

4085369.

KEGG

ldb:Ldb0101.

PATRIC

22215856. VBILacDel123523_0087.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG1052.

HOGENOM

HOG000136695.

KO

K03778.

OMA

GFGCKII.

ProtClustDB

CLSK912466.

Enzyme and pathway databases

BioCyc

LDEL390333:GIXG-99-MONOMER.

SABIO-RK

P26297.

Family and domain databases

Gene3D

3.40.50.720. 2 hits.

InterPro

IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_2_OHA_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Pfam

PF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
[Graphical view]

PROSITE

PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P26297.

Entry information

Entry name

LDHD_LACDA

Accession

Primary (citable) accession number: P26297
Secondary accession number(s): Q1G7V7

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 105 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program