9KL6
Crystal structure of NADP-specific glutamate dehydrogenase Gdh1 from Schizosaccharomyces pombe in complex with alpha-iminoglutarate and NADP+
Summary for 9KL6
| Entry DOI | 10.2210/pdb9kl6/pdb |
| Descriptor | NADP-specific glutamate dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, SULFATE ION, ... (6 entities in total) |
| Functional Keywords | glutamate dehydrogenase, nadp, rossmann fold, oxidoreductase |
| Biological source | Schizosaccharomyces pombe (fission yeast) |
| Total number of polymer chains | 1 |
| Total formula weight | 52315.70 |
| Authors | Tomita, T.,Yoshida, A.,Nishiyama, M. (deposition date: 2024-11-14, release date: 2025-07-30, Last modification date: 2025-08-06) |
| Primary citation | Wang, Y.F.,Tomita, T.,Yoshida, A.,Kosono, S.,Nishiyama, M. Phosphorylation-mediated regulation of the NADPH-dependent glutamate dehydrogenase, SpGdh1, from Schizosaccharomyces pombe. J.Biol.Chem., 301:110422-110422, 2025 Cited by PubMed Abstract: Glutamate dehydrogenase from the yeast Schizosaccharomyces pombe (SpGdh1) is a pivotal enzyme that catalyzes the conversion of 2-oxoglutarate and ammonium to glutamate using NADPH as a coenzyme. Although SpGdh1 is phosphorylated at several residues, the impact of phosphorylation on enzyme activity and the underlying molecular mechanisms remains unclear. To elucidate the phosphorylation-mediated regulation of SpGdh1, we determined the crystal structure of SpGdh1 binding 2-iminoglutarate (2-IG) and NADP. The results of the structural analysis revealed that four serine residues for phosphorylation were located near the active site. Ser252 directly interacted with the 2'-phosphate group of the adenine ribose moiety of NADP, suggesting that the phosphorylation of Ser252 interfered with NADP binding. To confirm this hypothesis, we prepared SpGdh1 phosphorylation-mimic (Ser to Glu) variants of SpGdh1 at these four Ser residues. The results of a kinetic analysis revealed that the replacement of these four residues increased the apparent K value and decreased catalytic efficiency, k/K.In contrast, substitutions decreased the apparent K value and increased catalytic efficiency, k/K. Therefore, the Ser to Glu replacement caused net shifts in the coenzyme specificities (NADPH to NADH and NADP to NAD) of 55- and 2900-fold, respectively. This is the first study to reveal the effects of the phosphorylation of SpGdh1 on its activity. PubMed: 40578557DOI: 10.1016/j.jbc.2025.110422 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.45 Å) |
Structure validation
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