DB code: D00456

CATH domain 3.40.50.720 : Rossmann fold
3.40.50.720 : Rossmann fold Catalytic domain
E.C. 1.1.1.28
CSA 1j49
M-CSA 1j49
MACiE

CATH domain Related DB codes (homologues)
3.40.50.720 : Rossmann fold S00543 S00551 S00552 S00553 S00602 S00604 S00605 S00608 S00610 S00625 S00319 S00328 S00329 S00330 S00331 S00332 D00457 D00458 S00324 S00320 S00325 S00326 S00327 D00459 S00335 S00336 S00334 T00219 S00339 D00513 D00001 D00002 D00003 D00005 D00007 D00008 D00010 D00012 D00017 D00018 D00023 D00027 D00028 D00031 D00032 D00033 D00034 D00035 D00037 D00048 D00071 D00476 D00481 D00482 D00490 D00492 D00494 D00545 D00601 D00603 D00604 D00605 D00615 D00845 D00857 D00858 M00161 M00171 M00210 T00002 T00010 T00011 T00015 T00227 T00247 T00408 T00414 D00827 D00262 D00274 D00275 M00035 T00109

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam RefSeq
P30901 D-lactate dehydrogenase
D-LDH
EC 1.1.1.28
D-specific D-2-hydroxyacid dehydrogenase
PF00389 (2-Hacid_dh)
PF02826 (2-Hacid_dh_C)
[Graphical View]
P26297 D-lactate dehydrogenase
D-LDH
EC 1.1.1.28
D-specific D-2-hydroxyacid dehydrogenase
PF00389 (2-Hacid_dh)
PF02826 (2-Hacid_dh_C)
[Graphical View]
YP_618304.1 (Protein)
NC_008054.1 (DNA/RNA sequence)

KEGG enzyme name
D-lactate dehydrogenase
lactic acid dehydrogenase
lactic acid dehydrogenase
D-specific lactic dehydrogenase
D-(-)-lactate dehydrogenase (NAD+)
D-lactic acid dehydrogenase
D-lactic dehydrogenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P26297 LDHD_LACDA (R)-lactate + NAD(+) = pyruvate + NADH. Homodimer.
P30901 LDHD_LACHE (R)-lactate + NAD(+) = pyruvate + NADH. Homodimer.

KEGG Pathways
Map code Pathways E.C.
MAP00620 Pyruvate metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00256 C00003 C00022 C00004 C00080
E.C.
Compound (R)-Lactate NAD+ Pyruvate NADH H+
Type carbohydrate,carboxyl group amide group,amine group,nucleotide carbohydrate,carboxyl group amide group,amine group,nucleotide others
ChEBI 42111
15846
32816
16908
15378
PubChem 61503
5893
1060
439153
1038
2dldA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2dldB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1j49A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1j49B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1j4aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1j4aB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1j4aC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1j4aD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2dldA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Analogue:OXM Unbound
2dldB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Analogue:OXM Unbound
1j49A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound
1j49B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound
1j4aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1j4aB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1j4aC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1j4aD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P30901 & literature [16], [17] & [20]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2dldA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2dldB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1j49A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1j49B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1j4aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1j4aB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1j4aC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1j4aD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2dldA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 206;ARG 236;ASP 260;GLU 265;HIS 297
2dldB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 206;ARG 236;ASP 260;GLU 265;HIS 297
1j49A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 206;ARG 236;ASP 260;GLU 265;HIS 297
1j49B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 206;ARG 236;ASP 260;GLU 265;HIS 297
1j4aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 206;ARG 236;ASP 260;GLU 265; mutant H297K
1j4aB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 206;ARG 236;ASP 260;GLU 265; mutant H297K
1j4aC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 206;ARG 236;ASP 260;GLU 265; mutant H297K
1j4aD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 206;ARG 236;ASP 260;GLU 265; mutant H297K

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[11]
[12]
Fig.6, p.936
[16]
[17]
Fig.6
[18]
p.653-655
[20]
[23]
p.113

References
[1]
Resource
Comments
Medline ID
PubMed ID 4291632
Journal Biochem Biophys Res Commun
Year 1967
Volume 26
Pages 679-85
Authors Garland RC, Kaplan NO
Title Salt-induced alteration of D(-) lactate dehydrogenase from Polyspondylium pallidum.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 4348014
Journal Arch Biochem Biophys
Year 1973
Volume 154
Pages 711-25
Authors Long GL, Kaplan NO
Title Diphosphopyridine nucleotide-linked D-lactate dehydrogenases from the horseshoe crab, Limulus polyphemus, and the seaworm, Nereis virens. II. Catalytic properties.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7074087
Journal Biochemistry
Year 1982
Volume 21
Pages 1307-12
Authors Morpeth FF, Massey V
Title Steady-state kinetic studies on D-lactate dehydrogenase from Megasphera elsdenii.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 6652095
Journal Biochim Biophys Acta
Year 1983
Volume 749
Pages 153-62
Authors Siebenaller JF, Orr TL, Olwin BB, Taylor SS
Title Comparison of the D-lactate stereospecific dehydrogenase of Limulus polyphemus with active-site regions of L-lactate dehydrogenases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 3248371
Journal Comp Biochem Physiol B
Year 1988
Volume 90
Pages 833-6
Authors Ward AP, al-Abidin NZ
Title Multiple molecular forms of Acanthamoeba lactic dehydrogenase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2610514
Journal Appl Biochem Biotechnol
Year 1989
Volume 22
Pages 169-79
Authors Simon ES, Plante R, Whitesides GM
Title D-lactate dehydrogenase. Substrate specificity and use as a catalyst in the synthesis of homochiral 2-hydroxy acids.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 2378905
Journal Biochim Biophys Acta
Year 1990
Volume 1040
Pages 84-8
Authors Denicola-Seoane A, Anderson BM
Title Nonpolar interactions in the maleimide inactivation of Haemophilus influenzae D-lactate dehydrogenase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 2117936
Journal Biol Chem Hoppe Seyler
Year 1990
Volume 371
Pages 515-9
Authors Hecht K, Langer T, Wrba A, Jaenicke R
Title Lactate dehydrogenase from the extreme halophilic archaebacterium Halobacterium marismortui.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 1567457
Journal Biochem Biophys Res Commun
Year 1992
Volume 184
Pages 60-6
Authors Kochhar S, Hunziker PE, Leong-Morgenthaler P, Hottinger H
Title Evolutionary relationship of NAD(+)-dependent D-lactate dehydrogenase: comparison of primary structure of 2-hydroxy acid dehydrogenases.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 8476420
Journal Biochem Biophys Res Commun
Year 1993
Volume 192
Pages 182-8
Authors Vinals C, Depiereux E, Feytmans E
Title Prediction of structurally conserved regions of D-specific hydroxy acid dehydrogenases by multiple alignment with formate dehydrogenase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 8349682
Journal J Biol Chem
Year 1993
Volume 268
Pages 18030-4
Authors Taguchi H, Ohta T
Title Histidine 296 is essential for the catalysis in Lactobacillus plantarum D-lactate dehydrogenase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 7961609
Journal J Biochem (Tokyo)
Year 1994
Volume 115
Pages 930-6
Authors Taguchi H, Ohta T
Title Essential role of arginine 235 in the substrate-binding of Lactobacillus plantarum D-lactate dehydrogenase.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 8289259
Journal J Mol Biol
Year 1994
Volume 235
Pages 370-1
Authors Nessler S, Le Bras G, Le Bras G, Garel JR
Title Crystallization of D-lactate dehydrogenase from Lactobacillus bulgaricus.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 7567953
Journal Proteins
Year 1995
Volume 21
Pages 307-18
Authors Vinals C, De Bolle X, Depiereux E, Feytmans E
Title Knowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure.
Related PDB 1dld
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 8955418
Journal J Bacteriol
Year 1996
Volume 178
Pages 7311-5
Authors Ferain T, Schanck AN, Delcour J
Title 13C nuclear magnetic resonance analysis of glucose and citrate end products in an ldhL-ldhD double-knockout strain of Lactobacillus plantarum.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 8740366
Journal Structure
Year 1996
Volume 4
Pages 437-47
Authors Stoll VS, Kimber MS, Pai EF
Title Insights into substrate binding by D-2-ketoacid dehydrogenases from the structure of Lactobacillus pentosus D-lactate dehydrogenase.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 9399585
Journal J Biochem (Tokyo)
Year 1997
Volume 122
Pages 802-9
Authors Taguchi H, Ohta T, Matsuzawa H
Title Involvement of Glu-264 and Arg-235 in the essential interaction between the catalytic imidazole and substrate for the D-lactate dehydrogenase catalysis.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 9126843
Journal J Mol Biol
Year 1997
Volume 267
Pages 640-60
Authors Dengler U, Niefind K, Kiess M, Schomburg D
Title Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 9605319
Journal Protein Sci
Year 1998
Volume 7
Pages 1147-55
Authors Stoll VS, Manohar AV, Gillon W, MacFarlane EL, Hynes RC, Pai EF
Title A thioredoxin fusion protein of VanH, a D-lactate dehydrogenase from Enterococcus faecium: cloning, expression, purification, kinetic analysis, and crystallization.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 10712593
Journal Eur J Biochem
Year 2000
Volume 267
Pages 1633-9
Authors Kochhar S, Lamzin VS, Razeto A, Delley M, Hottinger H, Germond JE
Title Roles of his205, his296, his303 and Asp259 in catalysis by NAD+-specific D-lactate dehydrogenase.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11826966
Journal Biosci Biotechnol Biochem
Year 2001
Volume 65
Pages 2695-700
Authors Fujita M, Tamegai H, Eguchi T, Kakinuma K
Title Novel substrate specificity of designer 3-isopropylmalate dehydrogenase derived from Thermus thermophilus HB8.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12127981
Journal Biochem Biophys Res Commun
Year 2002
Volume 295
Pages 910-6
Authors Flick MJ, Konieczny SF
Title Identification of putative mammalian D-lactate dehydrogenase enzymes.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 12054772
Journal J Mol Biol
Year 2002
Volume 318
Pages 109-19
Authors Razeto A, Kochhar S, Hottinger H, Dauter M, Wilson KS, Lamzin VS
Title Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus.
Related PDB 1j49 1j4a
Related UniProtKB

Comments
This enzyme may have a similar catalytic mechanism to that of glycerate dehydrogenase (D00457 in EzCatDB), as they share a similar active-site.

Created Updated
2004-12-01 2009-02-26