Modelisation of the dinucleotide-binding motives and key residues of glutamate dehydrogenase EC 1.4.1.4 with NADPH (NDP⁵⁶²) and Glu

A theoretical 3D structure of GDH4 from Ref was generated with the homology-modeling program ESyPred3D using as the template the structure of bovine GDH3 (PDB # 1HWZ).

The modelisation and the drawing of a putative structure of GDH4 was performed with the protein structure homology-modeling program DeepView (SwissPdb-Viewer).

1. Some interactions (plain lines in figure below) between the motif G³¹³AGNVA³¹⁸ or key residues and the coenzyme are indicated :

• NDP⁵⁶²AO3 - Gly³¹³CA
• NDP⁵⁶²AO1 - Asn³¹⁶ND2
• NDP⁵⁶²AO1 - Val³¹⁷N
• NDP⁵⁶²AO2 - Gly²⁴⁴N
• NDP⁵⁶²NC4 - Thr²⁸⁵OG1

2. The distances between the protonated carbon atom of the nicotinamide moiety (NDP⁵⁶²NC4) are too long for direct interactions with the motif G³¹³AGNVA³¹⁸.

3. However, this motif is stabilized by an internal H-bond Gly³¹⁵O - Ala³¹⁸N (dotted line).

4. Two distances (Glu⁵⁵⁷OE2 - Lys¹⁶⁶NZ and Glu⁵⁵⁷O - Lys¹⁹⁰NZ) are compatible with H-bond interactions between the enzyme and Glu.

5. The position of the motif G²⁶⁶VLTGKG²⁷² is shown with the potential H-bond Lys¹⁶⁶NZ - Thr²⁶⁹OG1.