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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1gdh

E.C. nameglycerate dehydrogenase
SpeciesHyphomicrobium methylovorum ()
E.C. Number (IntEnz) 1.1.1.29
CSA Homologues of 1gdhThere are 15 Homologs
CSA Entries With UniProtID P36234
CSA Entries With EC Number 1.1.1.29
PDBe Entry 1gdh
PDBSum Entry 1gdh
MACiE Entry 1gdh

Literature Report

IntroductionD-Glycerate dehydrogenase (GDH) catalyses the NADH-dependent reduction of hydroxypyruvate to D-glycerate. In the species Hyphomicrobium methylovorum, GDH operates in a specialised serine pathway in which formaldehyde is assimilated into cellular material. This enables H. methylovorum, and other methyltrophic bacteria to utilize one carbon compounds as sole sources of carbon and energy.
MechansimThe enzyme catalyses the hydride transfer from the NADH cofactor to the carbonyl of the hydroxypyruvate substrate, forming D-glycerate. The reduction is stereospecific, with the NADH cofactor orientated in such a way that the hydride is transferred to the Si face of the hydroxypyruvate substrate, forming only the D-glycerate isomer. The reaction is thought to involve a gaunidinium group and an imidazole ring coupled to a carboxylate side chain, where the histadine imidazole acts as a general acid towards the substrate and the arginine gaunidinium interacts with the substrate carboxylate group, orientating the substrate within the active site.
Reaction

Catalytic Sites for 1gdh

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA287288macie:sideChainThe residue acts as a general acid towards the substrate in concert with the hydride transfer step, donating a proton from the imidazole ring to the oxygen of the reacting carbonyl. The pKa of the imidazole ring is modified though hydrogen bonding to Glu269 as part of a His/Asp-like pair.
GluA269270macie:sideChainThe residue hydrogen bonds to the imidazole ring of His287, influencing the group's pKa and so enhancing proton transfer to the substrate, a role more commonly seen in a His/Asp pair.

Literature References

Notes:
Goldberg JD
Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution.
J Mol Biol 1994 236 1123-1140
PubMed: 8120891
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