Glycerate dehydrogenase

 

D-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 methyltrophic bacteria to utilise one carbon compounds as sole sources of carbon and energy.

 

Reference Protein and Structure

Sequence
P36234 UniProt (1.1.1.29) IPR006139 (Sequence Homologues) (PDB Homologues)
Biological species
Hyphomicrobium methylovorum (Bacteria) Uniprot
PDB
1gdh - CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION (2.4 Å) PDBe PDBsum 1gdh
Catalytic CATH Domains
3.40.50.720 CATHdb (see all for 1gdh)
Click To Show Structure

Enzyme Reaction (EC:1.1.1.29)

NADH(2-)
CHEBI:57945ChEBI
+
hydron
CHEBI:15378ChEBI
+
3-hydroxypyruvate
CHEBI:17180ChEBI
→
D-glycerate
CHEBI:16659ChEBI
+
NAD(1-)
CHEBI:57540ChEBI
Alternative enzyme names: D-glycerate dehydrogenase, Hydroxypyruvate dehydrogenase,

Enzyme Mechanism

Introduction

The 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.

Catalytic Residues Roles

UniProt PDB* (1gdh)
Arg241 Arg240(239)A The residue binds glycerate in the active site. electrostatic stabiliser
Glu270 Glu269(268)A The 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. electrostatic stabiliser
His288 His287(286)A The 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. proton acceptor, proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

aromatic unimolecular elimination by the conjugate base, bimolecular nucleophilic addition, overall product formed, overall reactant used, hydride transfer, proton transfer, native state of enzyme regenerated, inferred reaction step

References

  1. Goldberg JD et al. (1994), J Mol Biol, 236, 1123-1140. Crystal structure of a NAD-dependent d-glycerate dehydrogenase at 2·4 Å resolution. DOI:10.1016/0022-2836(94)90016-7. PMID:8120891.

Step 1. There is nucleophilic attack of a hydride from NADH to the reactive carbon of hydroxypyruvate. The si face of hydroxypyruvate is attacked to form D-glycerate. A proton is transferred from protonated His287 to the forming alkoxide of the product.

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Catalytic Residues Roles

Residue Roles
Glu269(268)A electrostatic stabiliser
Arg240(239)A electrostatic stabiliser
His287(286)A proton donor

Chemical Components

ingold: aromatic unimolecular elimination by the conjugate base, ingold: bimolecular nucleophilic addition, overall product formed, overall reactant used, hydride transfer, proton transfer

Step 2. In an inferred reaction step His287 is reprotonated to regenerate the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His287(286)A proton acceptor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1. There is nucleophilic attack of a hydride from NADH to the reactive carbon of hydroxypyruvate. The si face of hydroxypyruvate is attacked to form D-glycerate. A proton is transferred from protonated His287 to the forming alkoxide of the product.

Step 2. In an inferred reaction step His287 is reprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Anna Waters, Craig Porter, Gemma L. Holliday, Amelia Brasnett