4AJ3

3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and NADP - The pseudo-Michaelis complex

4AJ3 の概要

• エントリーDOI: 10.2210/pdb4aj3/pdb
• 関連するPDBエントリー: 4AJA 4AJB 4AJC 4AJR 4AJS
• 分子名称: NADP ISOCITRATE DEHYDROGENASE, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ISOCITRIC ACID, ... (5 entities in total)
• 機能のキーワード: oxidoreductase, oxidative beta-decarboxylation
• 由来する生物種: ESCHERICHIA COLI
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 46785.17

構造登録者

Goncalves, S.,Miller, S.P.,Carrondo, M.A.,Dean, A.M.,Matias, P.M. (登録日: 2012-02-15, 公開日: 2012-10-31, 最終更新日: 2023-12-20)

主引用文献

Goncalves, S.,Miller, S.P.,Carrondo, M.A.,Dean, A.M.,Matias, P.M.
Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase.
Biochemistry, 51:7098-, 2012

PubMed Abstract: NADP(+) dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) belongs to a large family of α-hydroxyacid oxidative β-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding β-decarboxylation to an enol intermediate followed by tautomerization to the final α-ketone product. A comprehensive view of the induced fit needed for catalysis is revealed on comparing the first "fully closed" crystal structures of a pseudo-Michaelis complex of wild-type Escherichia coli IDH (EcoIDH) and the "fully closed" reaction product complex of the K100M mutant with previously obtained "quasi-closed" and "open" conformations. Conserved catalytic residues, binding the nicotinamide ring of NADP(+) and the metal-bound substrate, move as rigid bodies during domain closure by a hinge motion that spans the central β-sheet in each monomer. Interactions established between Thr105 and Ser113, which flank the "phosphorylation loop", and the nicotinamide mononucleotide moiety of NADP(+) establish productive coenzyme binding. Electrostatic interactions of a Lys100-Leu103-Asn115-Glu336 tetrad play a pivotal role in assembling a catalytically competent active site. As predicted, Lys230* is positioned to deprotonate/reprotonate the α-hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following β-decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the α-hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism.

PubMed: 22891681
DOI: 10.1021/BI300483W

実験手法

X-RAY DIFFRACTION (1.9 Å)