8GRU

Crystal structure of a constitutively active mutant of the alpha beta heterodimer of human IDH3 in complex with ICT, NAD and Ca

8GRU の概要

• エントリーDOI: 10.2210/pdb8gru/pdb
• 分子名称: Human IDH3 alpha subunit, Isoform A of Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (5 entities in total)
• 機能のキーワード: isocitrate dehydrogenase, nad-dependent idh, assembly, allosteric regulation, oxidoreductase
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 154672.42

構造登録者

Sun, P.,Chen, X.,Ding, J. (登録日: 2022-09-02, 公開日: 2022-11-30, 最終更新日: 2023-11-29)

主引用文献

Chen, X.,Sun, P.,Liu, Y.,Shen, S.,Ma, T.,Ding, J.
Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction.
J.Biol.Chem., 298:102695-102695, 2022

PubMed Abstract: Human NAD-dependent isocitrate dehydrogenase or IDH3 (HsIDH3) catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the tricarboxylic acid cycle. It consists of three types of subunits (α, β, and γ) and exists and functions as the (αβαγ) heterooctamer. HsIDH3 is regulated allosterically and/or competitively by numerous metabolites including CIT, ADP, ATP, and NADH. Our previous studies have revealed the molecular basis for the activity and regulation of the αβ and αγ heterodimers. However, the molecular mechanism for the allosteric activation of the HsIDH3 holoenzyme remains elusive. In this work, we report the crystal structures of the αβ and αγ heterodimers and the (αβαγ) heterooctamer containing an α-Q139A mutation in the clasp domain, which renders all the heterodimers and the heterooctamer constitutively active in the absence of activators. Our structural analysis shows that the α-Q139A mutation alters the hydrogen-bonding network at the heterodimer-heterodimer interface in a manner similar to that in the activator-bound αγ heterodimer. This alteration not only stabilizes the active sites of both αβ and αγ heterodimers in active conformations but also induces conformational changes of the pseudo-allosteric site of the αβ heterodimer enabling it to bind activators. In addition, the αβ structure presents the first pseudo-Michaelis complex of HsIDH3, which allows us to identify the key residues involved in the binding of cofactor, substrate, and metal ion. Our structural and biochemical data together reveal new insights into the molecular mechanisms for allosteric regulation and the catalytic reaction of HsIDH3.

PubMed: 36375638
DOI: 10.1016/j.jbc.2022.102695

実験手法

X-RAY DIFFRACTION (2.847 Å)