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Figure 3 | Biology Direct

Figure 3

From: A computational analysis of the three isoforms of glutamate dehydrogenase reveals structural features of the isoform EC 1.4.1.4 supporting a key role in ammonium assimilation by plants

Figure 3

Modeling of the coenzyme-binding motifs and key residues of plant GDH4 with NADPH (NDP562) and Glu. Modeling of the coenzyme-binding motifs and key residues of GDH4 from Chlorella sorokiniana with NADPH (NDP562) and glutamate. Some interactions (plain lines) between the motif G313AGNVA318 or key residues and the coenzyme are indicated. NDP562AO3 – Gly313CA; NDP562AO1 – Asn316ND2; NDP562AO1 – Val317N; NDP562AO2 – Gly244N and NDP562NC4 – Thr285OG1. The distances between the protonated carbon atom of the nicotinamide moiety (NDP562NC4) are too long for direct interactions with the motif G313AGNVA318. However, this motif is stabilized by the H-bond Gly315O – Ala318N (dotted line). Two distances (Glu557OE2 – Lys166NZ and Glu557O – Lys190NZ) are compatible with salt-bridges between the enzyme and glutamate. The position of the motif G266VLTGKG272 is shown with the potential H-bond Lys166NZ – Thr269OG1. The figure was made with the program DeepView using a PDB-like file of GDH4 of Chlorella sorokiniana generated with the structure of bovine GDH3 (PDB # 1HWZ) as the template.

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