Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase.
Journal, issue, pages	Sci Rep, Vol. 14, Issue 1, Page 11165, Year 2024
Publish date	May 15, 2024
Authors	Taiki Wakabayashi / Mao Oide / Masayoshi Nakasako /
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 ...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.
External links	Sci Rep / PubMed:38750092 / PubMed Central
Methods	EM (single particle)
Resolution	2.6 - 2.96 Å
Structure data	38249 8xco EMDB-38249, PDB-8xco: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH in the initial stage of reaction Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.79 Å
Chemicals	ChemComp-NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE ChemComp-HOH: WATER ChemComp-NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE ChemComp-GGL: GAMMA-L-GLUTAMIC ACID ChemComp-AKG: 2-OXOGLUTARIC ACID ChemComp-NH4: AMMONIUM ION
Source	thermococcus profundus (archaea)
Keywords	OXIDOREDUCTASE / Complex / Coenzyme / NADPH / NADP+ / Glutamate / 2-oxoglutarate / ammonium ion / NADP