EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase.
ジャーナル・号・ページ	Sci Rep, Vol. 14, Issue 1, Page 11165, Year 2024
掲載日	2024年5月15日
著者	Taiki Wakabayashi / Mao Oide / Masayoshi Nakasako /
PubMed 要旨	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 ...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.
リンク	Sci Rep / PubMed:38750092 / PubMed Central
手法	EM (単粒子)
解像度	2.6 - 2.96 Å
構造データ	38249 8xco EMDB-38249, PDB-8xco: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH in the initial stage of reaction 手法: EM (単粒子) / 解像度: 2.64 Å 38250 8xcp EMDB-38250, PDB-8xcp: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the initial stage of reaction 手法: EM (単粒子) / 解像度: 2.64 Å 38251 8xcq EMDB-38251, PDB-8xcq: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the initial stage of reaction 手法: EM (単粒子) / 解像度: 2.6 Å 38252 8xcr EMDB-38252, PDB-8xcr: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus in complex with NADP and GLU in the initial stage of reaction 手法: EM (単粒子) / 解像度: 2.6 Å 38253 8xcs EMDB-38253, PDB-8xcs: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH, AKG and NH4 in the initial stage of reaction 手法: EM (単粒子) / 解像度: 2.63 Å 38254 8xct EMDB-38254, PDB-8xct: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.87 Å 38255 8xcu EMDB-38255, PDB-8xcu: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH, AKG and GLU in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.83 Å 38256 8xcv EMDB-38256, PDB-8xcv: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.83 Å 38257 8xcw EMDB-38257: Cryo-EM structure of glutamate dehydrogenase from thermococcus profundus incorporating NADPH and AKG in the steady stage of reaction PDB-8xcw: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH and AKG in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.87 Å 38258 8xcx EMDB-38258, PDB-8xcx: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.83 Å 38259 8xcy EMDB-38259, PDB-8xcy: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.91 Å 38260 8xcz EMDB-38260: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the steady stage of reaction PDB-8xcz: Cryo-EM structure of glutamate dehydrogenase from thermococcus profundus incorporating NADP and GLU in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.83 Å 38261 8xd0 EMDB-38261, PDB-8xd0: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH and AKG in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.83 Å 38262 8xd1 EMDB-38262, PDB-8xd1: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.96 Å 38263 8xd2 EMDB-38263, PDB-8xd2: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.64 Å 38264 8xd3 EMDB-38264, PDB-8xd3: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.87 Å 38265 8xd4 EMDB-38265, PDB-8xd4: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.87 Å 38266 8xd5 EMDB-38266, PDB-8xd5: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus in complex with NADP and GLU in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.75 Å 38267 8xd6 EMDB-38267, PDB-8xd6: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH, AKG and NH4 in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.79 Å
化合物	ChemComp-NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH ChemComp-HOH: WATER ChemComp-NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE ChemComp-GGL: GAMMA-L-GLUTAMIC ACID / グルタミン酸 ChemComp-AKG: 2-OXOGLUTARIC ACID / α-ケトグルタル酸 ChemComp-NH4: AMMONIUM ION / アンモニウム
由来	thermococcus profundus (古細菌)
キーワード	OXIDOREDUCTASE / Complex / Coenzyme / NADPH / NADP+ / Glutamate / 2-oxoglutarate / ammonium ion / NADP