Glycerol-3-phosphate dehydrogenase (NAD+)

 

Glycerol-3-phosphate dehydrogenase catalyses the interconversion of glycerol-3-phosphate (G3P) and Dihydroxyacetone-3-phosphate (DHAP), which is vital in the mitochondrial NAD/NADH shuttle. The dehydrogenase isolated from Leishmania mexicana (trypanosome) displays little sequence homology with the human system, thus may be a target for drug design.

 

Reference Protein and Structure

Sequence
P90551 UniProt (1.1.1.8) IPR006168 (Sequence Homologues) (PDB Homologues)
Biological species
Leishmania mexicana (Leishmania) Uniprot
PDB
1evy - CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEHYDROGENASE (1.75 Å) PDBe PDBsum 1evy
Catalytic CATH Domains
1.10.1040.10 CATHdb (see all for 1evy)
Click To Show Structure

Enzyme Reaction (EC:1.1.1.8)

NAD(1-)
CHEBI:57540ChEBI
+
sn-glycerol 3-phosphate(2-)
CHEBI:57597ChEBI
→
glycerone phosphate(2-)
CHEBI:57642ChEBI
+
hydron
CHEBI:15378ChEBI
+
NADH(2-)
CHEBI:57945ChEBI
Alternative enzyme names: Alpha-glycerol phosphate dehydrogenase (NAD), Alpha-glycerophosphate dehydrogenase (NAD), L-alpha-glycerol phosphate dehydrogenase, L-alpha-glycerophosphate dehydrogenase, L-glycerol phosphate dehydrogenase, L-glycerophosphate dehydrogenase, NAD-alpha-glycerophosphate dehydrogenase, NAD-L-glycerol-3-phosphate dehydrogenase, NAD-dependent glycerol phosphate dehydrogenase, NAD-dependent glycerol-3-phosphate dehydrogenase, NAD-linked glycerol 3-phosphate dehydrogenase, NADH-dihydroxyacetone phosphate reductase, Glycerol 1-phosphate dehydrogenase, Glycerol phosphate dehydrogenase (NAD), Glycerophosphate dehydrogenase (NAD), Hydroglycerophosphate dehydrogenase, Glycerol-3-phosphate dehydrogenase (NAD), L-glycerol-3-phosphate dehydrogenase,

Enzyme Mechanism

Introduction

Lys 210 acts as the general base for the extraction of a proton from G3P, forming an intermediate with negative charge on the oxygen, stabilised by contacts with Thr 267. This intermediate then collapses via hydride transfer to the NAD+ cofactor to form the DHAP product.

Catalytic Residues Roles

UniProt PDB* (1evy)
Thr267 Thr267A Makes favourable contacts with the negatively charged oxygen of the intermediate to stabilise the transition state. electrostatic stabiliser
Lys210 Lys210A Acts as a general base to extract a proton from G3P to form the charged intermediate thus facilitating hydride transfer from the substrate to NAD+ 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

proton transfer, intermediate formation, overall reactant used, aromatic bimolecular nucleophilic addition, hydride transfer, overall product formed, intermediate collapse, inferred reaction step, native state of enzyme regenerated

References

  1. Choe J et al. (2003), J Mol Biol, 329, 335-349. Leishmania mexicana Glycerol-3-phosphate Dehydrogenase Showed Conformational Changes Upon Binding a Bi-substrate Adduct. DOI:10.1016/s0022-2836(03)00421-2. PMID:12758080.
  2. Suresh S et al. (2000), Structure, 8, 541-552. A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana. DOI:10.1016/s0969-2126(00)00135-0. PMID:10801498.

Step 1. Lys210 abstracts a proton from the O-2 hydroxyl group of G3P.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr267A electrostatic stabiliser
Lys210A proton acceptor

Chemical Components

proton transfer, intermediate formation, overall reactant used

Step 2. A hydride is transferred from G3P to NAD+ in an aromatic bimolecular nucleophilic addition reaction and the product is formed.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

ingold: aromatic bimolecular nucleophilic addition, hydride transfer, overall product formed, intermediate collapse

Step 3. In an inferred reaction step Lys210 is deprotonated to regenerate the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys210A proton donor

Chemical Components

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

Step 1. Lys210 abstracts a proton from the O-2 hydroxyl group of G3P.

Step 2. A hydride is transferred from G3P to NAD+ in an aromatic bimolecular nucleophilic addition reaction and the product is formed.

Step 3. In an inferred reaction step Lys210 is deprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, Amelia Brasnett