EzCatDB: D00457
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DB codeD00457
CATH domainDomain 13.40.50.720 : Rossmann fold
Domain 23.40.50.720 : Rossmann foldCatalytic domain
E.C.1.1.1.29
CSA1gdh

CATH domainRelated DB codes (homologues)
3.40.50.720 : Rossmann foldS00543,S00551,S00552,S00553,S00602,S00604,S00605,S00608,S00610,S00625,S00319,S00328,S00329,S00330,S00331,S00332,D00456,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
UniProtKBKEGG

P36234
Protein nameGlycerate dehydrogenaseglycerate dehydrogenase
D-glycerate dehydrogenase
hydroxypyruvate reductase
SynonymsGDH
EC 1.1.1.29
NADH-dependent hydroxypyruvate reductase
HPR
Hydroxypyruvate dehydrogenase
Glyoxylate reductase
PfamPF00389 (2-Hacid_dh)
PF02826 (2-Hacid_dh_C)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00260Glycine, serine and threonine metabolism
MAP00630Glyoxylate and dicarboxylate metabolism

UniProtKB:Accession NumberP36234
Entry nameDHGY_HYPME
Activity(R)-glycerate + NAD(+) = hydroxypyruvate + NADH.
SubunitHomodimer.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00258C00003C00168C00004
Compound(R)-GlycerateNAD+HydroxypyruvateNADH
Typecarbohydrate,carboxyl groupamide group,amine group,nucleotidecarbohydrate,carboxyl groupamide group,amine group,nucleotide
ChEBI32398
15846
30841
16908
PubChem439194
5893
964
439153
            
1gdhA01UnboundUnboundUnboundUnbound
1gdhB01UnboundUnboundUnboundUnbound
1gdhA02UnboundUnboundUnboundUnbound
1gdhB02UnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P36234
pdbCatalytic residues
         
1gdhA01 
1gdhB01 
1gdhA02ARG 240;GLU 269;HIS 287
1gdhB02ARG 240;GLU 269;HIS 287

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.1549-1551
[5]p.1133-1136, Fig.122

references
[1]
PubMed ID14154
JournalJ Biol Chem
Year1977
Volume252
Pages1539-51
AuthorsDubrow R, Pizer LI
TitleTransient kinetic and deuterium isotope effect studies on the catalytic mechanism of phosphoglycerate dehydrogenase.
[2]
PubMed ID2689175
JournalEur J Biochem
Year1989
Volume186
Pages355-9
AuthorsVan Schaftingen E, Draye JP, Van Hoof F
TitleCoenzyme specificity of mammalian liver D-glycerate dehydrogenase.
[3]
CommentsCHARACTERIZATION
Medline ID90306024
PubMed ID2114287
JournalEur J Biochem
Year1990
Volume190
Pages279-84
AuthorsIzumi Y, Yoshida T, Kanzaki H, Toki S, Miyazaki SS, Yamada H
TitlePurification and characterization of hydroxypyruvate reductase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2.
Related UniProtKBP36234
[4]
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.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
Medline ID94166078
PubMed ID8120891
JournalJ Mol Biol
Year1994
Volume236
Pages1123-40
AuthorsGoldberg JD, Yoshida T, Brick P
TitleCrystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution.
Related PDB1gdh
Related UniProtKBP36234

comments
This enzyme may have a similar catalytic mechanism to that of lactate dehydrogenase (D00456 in EzCatDB), as they share a similar active-site.

createdupdated
2004-03-252009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
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