8XCS

Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH, AKG and NH4 in the initial stage of reaction

8XCS の概要

• エントリーDOI: 10.2210/pdb8xcs/pdb
• EMDBエントリー: 38253
• 分子名称: Glutamate dehydrogenase, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 2-OXOGLUTARIC ACID, ... (5 entities in total)
• 機能のキーワード: complex, coenzyme, nadph, 2-oxoglutarate, ammonium ion, oxidoreductase
• 由来する生物種: Thermococcus profundus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 47668.03

構造登録者

Wakabayashi, T.,Oide, M.,Nakasako, M. (登録日: 2023-12-10, 公開日: 2023-12-27, 最終更新日: 2024-06-19)

主引用文献

Wakabayashi, T.,Oide, M.,Nakasako, M.
CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase.
Sci Rep, 14:11165-11165, 2024

PubMed Abstract: Kinetic aspects of enzymatic reactions are described by equations based on the Michaelis-Menten theory for the initial stage. However, the kinetic parameters provide little information on the atomic mechanism of the reaction. In this study, we analyzed structures of glutamate dehydrogenase in the initial and steady stages of the reaction using cryoEM at near-atomic resolution. In the initial stage, four metastable conformations displayed different domain motions and cofactor/ligand association modes. The most striking finding was that the enzyme-cofactor-substrate complex, treated as a single state in the enzyme kinetic theory, comprised at least three different metastable conformations. In the steady stage, seven conformations, including derivatives from the four conformations in the initial stage, made the reaction pathway complicated. Based on the visualized conformations, we discussed stage-dependent pathways to illustrate the dynamics of the enzyme in action.

PubMed: 38750092
DOI: 10.1038/s41598-024-61793-x

実験手法

ELECTRON MICROSCOPY (2.63 Å)