SCAN:Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase
Pedro Matias Head of Industry and Medicine Applied Crystallography Lab.
| When |
21 Nov, 2012
from
12:00 pm to 01:00 pm |
|---|---|
| Where | Auditorium |
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ITQB Scan Seminar
Title: Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase
Speaker: Pedro Matias
From: Head of Industry and Medicine Applied Crystallography Laboratory
Abstract:
NADP+ dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) belongs to a large family of -hydroxyacid oxidative -decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding -decarboxylation to an enol intermediate followed by tautomerization to the final -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 -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 -hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following -decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the -hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism.
