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 and crystal structure analyses reveal the indirect role played by Trp89 in glutamate dehydrogenase enzymatic reactions.
ジャーナル・号・ページ	FEBS J, Vol. 292, Issue 8, Page 2071-2094, Year 2025
掲載日	2025年2月1日
著者	Taiki Wakabayashi / Yuka Matsui / Masayoshi Nakasako /
PubMed 要旨	Glutamate dehydrogenase from Thermococcus profundus is a homo-hexameric enzyme that catalyzes the reversible deamination of glutamate to 2-oxoglutarate in the presence of a cofactor. In each subunit, ...Glutamate dehydrogenase from Thermococcus profundus is a homo-hexameric enzyme that catalyzes the reversible deamination of glutamate to 2-oxoglutarate in the presence of a cofactor. In each subunit, a large active-site cleft is formed between the two functional domains, one of which displays motion to open and close the cleft. Trp89 in the cleft displays two sidechain conformers in the open cleft and a single conformer in the closed cleft. To reveal the role of the Trp89 sidechain in the domain motion, we mutated Trp89 to phenylalanine. Despite the Trp89 sidechain being located away from the reaction center, the catalytic constant decreased to 1/38-fold of that of the wild-type without a fatal reduction of the affinities to the cofactor and ligand molecules. To understand the molecular mechanism underlying this reduction, we determined the crystal structure in the unliganded state and the metastable conformations appearing in the steady stage of the reaction using cryo-electron microscopy (cryoEM). The four identified metastable conformations were similar to the three conformations observed in the wild-type, but their populations were different from those of the wild-type. In addition, a conformation with a completely closed active-site cleft necessary for the reaction to proceed was quite rare. The crystal structure and the four metastable conformations suggested that the reduction in the catalytic constant could be attributed to changes in the interactions between Gln13 and the 89th side chains, preventing the closing domain motion.
リンク	FEBS J / PubMed:39891504 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.028 - 2.64 Å
構造データ	60266 8znb EMDB-60266, PDB-8znb: Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.53 Å 60267 8znc EMDB-60267, PDB-8znc: Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH, AKG in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.41 Å 60268 8znd EMDB-60268, PDB-8znd: Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH and a substrate in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.53 Å 60269 8zne EMDB-60269, PDB-8zne: Cryo-EM structure of W89F mutated 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: 2.64 Å 60270 8zng EMDB-60270, PDB-8zng: Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH and AKG in the steady stage of reaction 手法: EM (単粒子) / 解像度: 2.5 Å PDB-8zmu: GLUTAMATE DEHYDROGENASE (W89F-MUTANT) FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGANDED STATE 手法: X-RAY DIFFRACTION / 解像度: 2.028 Å
化合物	ChemComp-SO4: SULFATE ION / 硫酸ジアニオン ChemComp-ACY: ACETIC ACID / 酢酸 ChemComp-GOL: GLYCEROL / グリセロ-ル ChemComp-NA: Unknown entry / ナトリウムカチオン ChemComp-HOH: WATER ChemComp-NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH ChemComp-AKG: 2-OXOGLUTARIC ACID / α-ケトグルタル酸 ChemComp-NH4: AMMONIUM ION / アンモニウム ChemComp-NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE ChemComp-GLU: GLUTAMIC ACID / グルタミン酸
由来	thermococcus profundus (古細菌)
キーワード	OXIDOREDUCTASE / Complex / NADPH / Mutant / 2-oxoglutarate / substrate / NADP / Glutamate