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	Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy.
ジャーナル・号・ページ	FEBS J, Vol. 290, Issue 23, Page 5514-5535, Year 2023
掲載日	2023年9月11日
著者	Taiki Wakabayashi / Mao Oide / Takayuki Kato / Masayoshi Nakasako /
PubMed 要旨	The structure of hexameric glutamate dehydrogenase (GDH) in the presence of the coenzyme nicotinamide adenine dinucleotide phosphate (NADP) was visualized using cryogenic transmission electron ...The structure of hexameric glutamate dehydrogenase (GDH) in the presence of the coenzyme nicotinamide adenine dinucleotide phosphate (NADP) was visualized using cryogenic transmission electron microscopy to investigate the ligand-binding pathways to the active site of the enzyme. Each subunit of GDH comprises one hexamer-forming core domain and one nucleotide-binding domain (NAD domain), which spontaneously opens and closes the active-site cleft situated between the two domains. In the presence of NADP, the potential map of GDH hexamer, assuming D3 symmetry, was determined at a resolution of 2.4 Å, but the NAD domain was blurred due to the conformational variety. After focused classification with respect to the NAD domain, the potential maps interpreted as NADP molecules appeared at five different sites in the active-site cleft. The subunits associated with NADP molecules were close to one of the four metastable conformations in the unliganded state. Three of the five binding sites suggested a pathway of NADP molecules to approach the active-site cleft for initiating the enzymatic reaction. The other two binding modes may rarely appear in the presence of glutamate, as demonstrated by the reaction kinetics. Based on the visualized structures and the results from the enzymatic kinetics, we discussed the binding modes of NADP to GDH in the absence and presence of glutamate.
リンク	FEBS J / PubMed:37682540
手法	EM (単粒子)
解像度	3.08 - 3.29 Å
構造データ	34805 8hho EMDB-34805, PDB-8hho: cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP 手法: EM (単粒子) / 解像度: 3.2 Å 34826 8hiq EMDB-34826, PDB-8hiq: cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP 手法: EM (単粒子) / 解像度: 3.2 Å 34830 8hiz EMDB-34830, PDB-8hiz: cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP 手法: EM (単粒子) / 解像度: 3.08 Å 34831 8hj3 EMDB-34831, PDB-8hj3: cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP 手法: EM (単粒子) / 解像度: 3.29 Å 34835 8hj9 EMDB-34835, PDB-8hj9: cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP 手法: EM (単粒子) / 解像度: 3.12 Å
化合物	ChemComp-NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / ニコチンアミドアデニンジヌクレオチドリン酸
由来	thermococcus profundus (古細菌)
キーワード	OXIDOREDUCTASE (酸化還元酵素) / Complex / Coenzyme (補因子) / NADP (ニコチンアミドアデニンジヌクレオチドリン酸)