1N1E

Crystal structure of Leishmania mexicana Glycerol-3-phosphate dehydrogenase complexed with DHAP and NAD

Summary for 1N1E

• Entry DOI: 10.2210/pdb1n1e/pdb
• Descriptor: glycerol-3-phosphate dehydrogenase, ADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) P'-5'-ESTER WITH 3-(AMINOCARBONYL)-4-(1-HYDROXYL-2-OXO-3-PHOSPHONOOXY-PROPYL)-1-BETA-D-RIBOFURANOSYLPYRIDINIUM INNER SALT (3 entities in total)
• Functional Keywords: nad binding domain, oxidoreductase
• Biological source: Leishmania mexicana
• Cellular location: Glycosome: P90551
• Total number of polymer chains: 2
• Total formula weight: 80298.59

Authors

Choe, J.,Hol, W.G.J. (deposition date: 2002-10-17, release date: 2003-05-27, Last modification date: 2024-02-14)

Primary citation

Choe, J.,Guerra, D.,Michels, P.A.M.,Hol, W.G.J.
Leishmania mexicana Glycerol-3-phosphate Dehydrogenase Showed Conformational Changes Upon Binding a Bi-substrate Adduct
J.Mol.Biol., 320:335-349, 2003

PubMed Abstract: Certain pathogenic trypanosomatids are highly dependent on glycolysis for ATP production, and hence their glycolytic enzymes, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. The ternary complex structure of Leishmania mexicana GPDH (LmGPDH) with dihydroxyacetone phosphate (DHAP) and NAD(+) was determined to 1.9A resolution as a further step towards understanding this enzyme's mode of action. When compared with the apo and binary complex structures, the ternary complex structure shows an 11 degrees hinge-bending motion of the C-terminal domain with respect to the N-terminal domain. In addition, residues in the C-terminal domain involved in catalysis or substrates binding show significant movements and a previously invisible five-residue loop region becomes well ordered and participates in NAD(+) binding. Unexpectedly, DHAP and NAD(+) appear to form a covalent bond, producing an adduct in the active site of LmGPDH. Modeling a ternary complex glycerol 3-phosphate (G3P) and NAD(+) with LmGPDH identified ten active site residues that are highly conserved among all GPDHs. Two lysine residues, Lys125 and Lys210, that are presumed to be critical in catalysis, were mutated resulting in greatly reduced catalytic activity. Comparison with other structurally related enzymes found by the program DALI suggested Lys210 as a key catalytic residue, which is located on a structurally conserved alpha-helix. From the results of site-directed mutagenesis, molecular modeling and comparison with related dehydrogenases, a catalytic mechanism of LmGPDH and a possible evolutionary scenario of this group of dehydrogenases are proposed.

PubMed: 12758080
DOI: 10.1016/S0022-2836(03)00421-2

Experimental method

X-RAY DIFFRACTION (1.9 Å)