4AJC

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, calcium(II) and adenine nucleotide phosphate

Summary for 4AJC

• Entry DOI: 10.2210/pdb4ajc/pdb
• Related: 4AJ3 4AJA 4AJB
• Descriptor: NADP ISOCITRATE DEHYDROGENASE, ADENOSINE-2'-5'-DIPHOSPHATE, 2-OXOGLUTARIC ACID, ... (6 entities in total)
• Functional Keywords: oxidoreductase, oxidative beta-decarboxylation
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 1
• Total formula weight: 46521.02

Authors

Goncalves, S.,Miller, S.P.,Carrondo, M.A.,Dean, A.M.,Matias, P.M. (deposition date: 2012-02-16, release date: 2012-10-31, Last modification date: 2023-12-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.3 Å)