DB code: D00457

CATH domain 3.40.50.720 : Rossmann fold
3.40.50.720 : Rossmann fold Catalytic domain
E.C. 1.1.1.29
CSA 1gdh
M-CSA 1gdh
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 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P36234 Glycerate dehydrogenase
GDH
EC 1.1.1.29
NADH-dependent hydroxypyruvate reductase
HPR
Hydroxypyruvate dehydrogenase
Glyoxylate reductase
PF00389 (2-Hacid_dh)
PF02826 (2-Hacid_dh_C)
[Graphical View]

KEGG enzyme name
glycerate dehydrogenase
D-glycerate dehydrogenase
hydroxypyruvate reductase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P36234 DHGY_HYPME (R)-glycerate + NAD(+) = hydroxypyruvate + NADH. Homodimer.

KEGG Pathways
Map code Pathways E.C.
MAP00630 Glyoxylate and dicarboxylate metabolism
MAP00260 Glycine, serine and threonine metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00258 C00003 C00168 C00004
E.C.
Compound (R)-Glycerate NAD+ Hydroxypyruvate NADH
Type carbohydrate,carboxyl group amide group,amine group,nucleotide carbohydrate,carboxyl group amide group,amine group,nucleotide
ChEBI 32398
15846
30841
16908
PubChem 439194
5893
964
439153
1gdhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1gdhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1gdhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1gdhB02 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;P36234

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1gdhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gdhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1gdhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 240;GLU 269;HIS 287
1gdhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 240;GLU 269;HIS 287

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.1549-1551
[5]
p.1133-1136, Fig.12 2

References
[1]
Resource
Comments
Medline ID
PubMed ID 14154
Journal J Biol Chem
Year 1977
Volume 252
Pages 1539-51
Authors Dubrow R, Pizer LI
Title Transient kinetic and deuterium isotope effect studies on the catalytic mechanism of phosphoglycerate dehydrogenase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2689175
Journal Eur J Biochem
Year 1989
Volume 186
Pages 355-9
Authors Van Schaftingen E, Draye JP, Van Hoof F
Title Coenzyme specificity of mammalian liver D-glycerate dehydrogenase.
Related PDB
Related UniProtKB
[3]
Resource
Comments CHARACTERIZATION
Medline ID 90306024
PubMed ID 2114287
Journal Eur J Biochem
Year 1990
Volume 190
Pages 279-84
Authors Izumi Y, Yoshida T, Kanzaki H, Toki S, Miyazaki SS, Yamada H
Title Purification and characterization of hydroxypyruvate reductase from a serine-producing methylotroph, Hyphomicrobium methylovorum GM2.
Related PDB
Related UniProtKB P36234
[4]
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
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
Medline ID 94166078
PubMed ID 8120891
Journal J Mol Biol
Year 1994
Volume 236
Pages 1123-40
Authors Goldberg JD, Yoshida T, Brick P
Title Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution.
Related PDB 1gdh
Related UniProtKB P36234

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

Created Updated
2004-03-25 2009-02-26