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	Conformational flexibility associated with remote residues regulates the kinetic properties of glutamate dehydrogenase.
ジャーナル・号・ページ	Protein Sci, Vol. 34, Issue 3, Page e70038, Year 2025
掲載日	2025年2月21日
著者	Barsa Kanchan Jyotshna Godsora / Parijat Das / Prasoon Kumar Mishra / Anjali Sairaman / Sandip Kaledhonkar / Narayan S Punekar / Prasenjit Bhaumik /
PubMed 要旨	Glutamate dehydrogenase (GDH) is a pivotal metabolic enzyme in all living organisms, and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric ...Glutamate dehydrogenase (GDH) is a pivotal metabolic enzyme in all living organisms, and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric communication during the homotropic effect in GDHs remains poorly understood. In this study, we examined two homologous GDHs, Aspergillus niger GDH (AnGDH) and Aspergillus terreus GDH (AtGDH), with differing substrate utilization kinetics to uncover the factors driving their distinct behavior. We report the crystal structures and first-ever cryo-EM structures of apo- AtGDH and AnGDH that captured arrays of conformational ensembles. A wider mouth opening (~ 21 Å) is observed for the cooperative AnGDH as compared to the non-cooperative AtGDH (~17 Å) in their apo states. A network of interactions related to the substitutions in Domain II influence structural flexibility in these GDHs. Remarkably, we have identified a distant substitution (R246 to S) in Domain II, as a part of this network, which can impact the mouth opening and converts non-cooperative AtGDH into a cooperative enzyme. Our study demonstrates that remote residues can influence structural and kinetic properties in homologous GDHs.
リンク	Protein Sci / PubMed:39981924 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.05 - 3.65 Å
構造データ	39722 8z1c EMDB-39722, PDB-8z1c: Cryo-EM structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the closed conformation (form 1) 手法: EM (単粒子) / 解像度: 3.15 Å 39730 8z1m EMDB-39730, PDB-8z1m: Cryo-EM structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the partially closed conformation (form 2) 手法: EM (単粒子) / 解像度: 3.25 Å 39731 8z1n EMDB-39731, PDB-8z1n: Cryo-EM structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the closed conformation (form 2) 手法: EM (単粒子) / 解像度: 3.18 Å 39732 8z1o EMDB-39732, PDB-8z1o: Cryo-EM structure of apo Aspergillus niger glutamate dehydrogenase (AnGDH) in the closed conformation 手法: EM (単粒子) / 解像度: 3.6 Å 39744 8z2f EMDB-39744, PDB-8z2f: Cryo-EM structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the partially closed conformation (form 1) 手法: EM (単粒子) / 解像度: 3.65 Å PDB-8z29: Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) deletion mutant (T262-A263) 手法: X-RAY DIFFRACTION / 解像度: 2.85 Å PDB-8z2a: Crystal structure of Aspergillus terreus glutamate dehydrogenase (AtGDH) with sequential mutations 手法: X-RAY DIFFRACTION / 解像度: 3.1 Å PDB-8z2b: Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the partially closed conformation (form II) 手法: X-RAY DIFFRACTION / 解像度: 2.85 Å PDB-8z2c: Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) with open and partially closed conformations (form I) 手法: X-RAY DIFFRACTION / 解像度: 2.05 Å
化合物	ChemComp-CL: Unknown entry / クロリド ChemComp-HOH: WATER ChemComp-ACT: ACETATE ION / 酢酸イオン
由来	aspergillus terreus (カビ) aspergillus niger (黒麹菌)
キーワード	OXIDOREDUCTASE / glutamate dehydrogenase / allostery / cooperativity / Aspergillus / cryo-EM / domain dynamics