EzCatDB: D00456

DB codeD00456
CATH domainDomain 13.40.50.720
Domain 23.40.50.720Catalytic domain
E.C.1.1.1.28
CSA1j49

CATH domainRelated DB codes (homologues)
3.40.50.720S00543,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

Enzyme Name
Swiss-protKEGG

P30901P26297
Protein nameD-lactate dehydrogenaseD-lactate dehydrogenaseD-lactate dehydrogenase
lactic acid dehydrogenase
lactic acid dehydrogenase
D-specific lactic dehydrogenase
D-(-)-lactate dehydrogenase (NAD+)
D-lactic acid dehydrogenase
D-lactic dehydrogenase
SynonymsD-LDH
EC 1.1.1.28
D-specific D-2-hydroxyacid dehydrogenase
D-LDH
EC 1.1.1.28
D-specific D-2-hydroxyacid dehydrogenase

KEGG pathways
MAP codePathways
MAP00620Pyruvate metabolism

Swiss-prot:Accession NumberP30901P26297
Entry nameLDHD_LACHELDHD_LACDA
Activity(R)-lactate + NAD(+) = pyruvate + NADH.(R)-lactate + NAD(+) = pyruvate + NADH.
SubunitHomodimer.Homodimer.
Subcellular location

Cofactor



SubstratesProducts
KEGG-idC00256C00003C00022C00004C00080
Compound(R)-LactateNAD+PyruvateNADHH+
Typecarbohydrate,carboxyl groupamide group,amine group,nucleotidecarbohydrate,carboxyl groupamide group,amine group,nucleotideothers
2dldA01UnboundUnboundUnboundUnbound
2dldB01UnboundUnboundUnboundUnbound
1j49A01UnboundUnboundUnboundUnbound
1j49B01UnboundUnboundUnboundUnbound
1j4aA01UnboundUnboundUnboundUnbound
1j4aB01UnboundUnboundUnboundUnbound
1j4aC01UnboundUnboundUnboundUnbound
1j4aD01UnboundUnboundUnboundUnbound
2dldA02UnboundBound:NADAnalogue:OXMUnbound
2dldB02UnboundBound:NADAnalogue:OXMUnbound
1j49A02UnboundBound:NADUnboundUnbound
1j49B02UnboundBound:NADUnboundUnbound
1j4aA02UnboundUnboundUnboundUnbound
1j4aB02UnboundUnboundUnboundUnbound
1j4aC02UnboundUnboundUnboundUnbound
1j4aD02UnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P30901 & literature [16], [17] & [20]
pdbCatalytic residuescomment
2dldA01

2dldB01

1j49A01

1j49B01

1j4aA01

1j4aB01

1j4aC01

1j4aD01

2dldA02HIS 206;ARG 236;ASP 260;GLU 265;HIS 297

2dldB02HIS 206;ARG 236;ASP 260;GLU 265;HIS 297

1j49A02HIS 206;ARG 236;ASP 260;GLU 265;HIS 297

1j49B02HIS 206;ARG 236;ASP 260;GLU 265;HIS 297

1j4aA02HIS 206;ARG 236;ASP 260;GLU 265;       
mutant H297K
1j4aB02HIS 206;ARG 236;ASP 260;GLU 265;       
mutant H297K
1j4aC02HIS 206;ARG 236;ASP 260;GLU 265;       
mutant H297K
1j4aD02HIS 206;ARG 236;ASP 260;GLU 265;       
mutant H297K

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[11]

[12]Fig.6, p.936
[16]

[17]Fig.6
[18]p.653-655
[20]

[23]p.113

references
[1]
PubMed ID4291632
JournalBiochem Biophys Res Commun
Year1967
Volume26
Pages679-85
AuthorsGarland RC, Kaplan NO
TitleSalt-induced alteration of D(-) lactate dehydrogenase from Polyspondylium pallidum.
[2]
PubMed ID4348014
JournalArch Biochem Biophys
Year1973
Volume154
Pages711-25
AuthorsLong GL, Kaplan NO
TitleDiphosphopyridine nucleotide-linked D-lactate dehydrogenases from the horseshoe crab, Limulus polyphemus, and the seaworm, Nereis virens. II. Catalytic properties.
[3]
PubMed ID7074087
JournalBiochemistry
Year1982
Volume21
Pages1307-12
AuthorsMorpeth FF, Massey V
TitleSteady-state kinetic studies on D-lactate dehydrogenase from Megasphera elsdenii.
[4]
PubMed ID6652095
JournalBiochim Biophys Acta
Year1983
Volume749
Pages153-62
AuthorsSiebenaller JF, Orr TL, Olwin BB, Taylor SS
TitleComparison of the D-lactate stereospecific dehydrogenase of Limulus polyphemus with active-site regions of L-lactate dehydrogenases.
[5]
PubMed ID3248371
JournalComp Biochem Physiol B
Year1988
Volume90
Pages833-6
AuthorsWard AP, al-Abidin NZ
TitleMultiple molecular forms of Acanthamoeba lactic dehydrogenase.
[6]
PubMed ID2610514
JournalAppl Biochem Biotechnol
Year1989
Volume22
Pages169-79
AuthorsSimon ES, Plante R, Whitesides GM
TitleD-lactate dehydrogenase. Substrate specificity and use as a catalyst in the synthesis of homochiral 2-hydroxy acids.
[7]
PubMed ID2378905
JournalBiochim Biophys Acta
Year1990
Volume1040
Pages84-8
AuthorsDenicola-Seoane A, Anderson BM
TitleNonpolar interactions in the maleimide inactivation of Haemophilus influenzae D-lactate dehydrogenase.
[8]
PubMed ID2117936
JournalBiol Chem Hoppe Seyler
Year1990
Volume371
Pages515-9
AuthorsHecht K, Langer T, Wrba A, Jaenicke R
TitleLactate dehydrogenase from the extreme halophilic archaebacterium Halobacterium marismortui.
[9]
PubMed ID1567457
JournalBiochem Biophys Res Commun
Year1992
Volume184
Pages60-6
AuthorsKochhar S, Hunziker PE, Leong-Morgenthaler P, Hottinger H
TitleEvolutionary relationship of NAD(+)-dependent D-lactate dehydrogenase: comparison of primary structure of 2-hydroxy acid dehydrogenases.
[10]
PubMed ID8476420
JournalBiochem Biophys Res Commun
Year1993
Volume192
Pages182-8
AuthorsVinals C, Depiereux E, Feytmans E
TitlePrediction of structurally conserved regions of D-specific hydroxy acid dehydrogenases by multiple alignment with formate dehydrogenase.
[11]
PubMed ID8349682
JournalJ Biol Chem
Year1993
Volume268
Pages18030-4
AuthorsTaguchi H, Ohta T
TitleHistidine 296 is essential for the catalysis in Lactobacillus plantarum D-lactate dehydrogenase.
[12]
PubMed ID7961609
JournalJ Biochem (Tokyo)
Year1994
Volume115
Pages930-6
AuthorsTaguchi H, Ohta T
TitleEssential role of arginine 235 in the substrate-binding of Lactobacillus plantarum D-lactate dehydrogenase.
[13]
PubMed ID8289259
JournalJ Mol Biol
Year1994
Volume235
Pages370-1
AuthorsNessler S, Le Bras G, Le Bras G, Garel JR
TitleCrystallization of D-lactate dehydrogenase from Lactobacillus bulgaricus.
[14]
PubMed ID7567953
JournalProteins
Year1995
Volume21
Pages307-18
AuthorsVinals C, De Bolle X, Depiereux E, Feytmans E
TitleKnowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure.
Related PDB1dld
[15]
PubMed ID8955418
JournalJ Bacteriol
Year1996
Volume178
Pages7311-5
AuthorsFerain T, Schanck AN, Delcour J
Title13C nuclear magnetic resonance analysis of glucose and citrate end products in an ldhL-ldhD double-knockout strain of Lactobacillus plantarum.
[16]
PubMed ID8740366
JournalStructure
Year1996
Volume4
Pages437-47
AuthorsStoll VS, Kimber MS, Pai EF
TitleInsights into substrate binding by D-2-ketoacid dehydrogenases from the structure of Lactobacillus pentosus D-lactate dehydrogenase.
[17]
PubMed ID9399585
JournalJ Biochem (Tokyo)
Year1997
Volume122
Pages802-9
AuthorsTaguchi H, Ohta T, Matsuzawa H
TitleInvolvement of Glu-264 and Arg-235 in the essential interaction between the catalytic imidazole and substrate for the D-lactate dehydrogenase catalysis.
[18]
PubMed ID9126843
JournalJ Mol Biol
Year1997
Volume267
Pages640-60
AuthorsDengler U, Niefind K, Kiess M, Schomburg D
TitleCrystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution.
[19]
PubMed ID9605319
JournalProtein Sci
Year1998
Volume7
Pages1147-55
AuthorsStoll VS, Manohar AV, Gillon W, MacFarlane EL, Hynes RC, Pai EF
TitleA thioredoxin fusion protein of VanH, a D-lactate dehydrogenase from Enterococcus faecium: cloning, expression, purification, kinetic analysis, and crystallization.
[20]
PubMed ID10712593
JournalEur J Biochem
Year2000
Volume267
Pages1633-9
AuthorsKochhar S, Lamzin VS, Razeto A, Delley M, Hottinger H, Germond JE
TitleRoles of his205, his296, his303 and Asp259 in catalysis by NAD+-specific D-lactate dehydrogenase.
[21]
PubMed ID11826966
JournalBiosci Biotechnol Biochem
Year2001
Volume65
Pages2695-700
AuthorsFujita M, Tamegai H, Eguchi T, Kakinuma K
TitleNovel substrate specificity of designer 3-isopropylmalate dehydrogenase derived from Thermus thermophilus HB8.
[22]
PubMed ID12127981
JournalBiochem Biophys Res Commun
Year2002
Volume295
Pages910-6
AuthorsFlick MJ, Konieczny SF
TitleIdentification of putative mammalian D-lactate dehydrogenase enzymes.
[23]
PubMed ID12054772
JournalJ Mol Biol
Year2002
Volume318
Pages109-19
AuthorsRazeto A, Kochhar S, Hottinger H, Dauter M, Wilson KS, Lamzin VS
TitleDomain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus.
Related PDB1j49,1j4a

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

createdupdated
2004-12-012009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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