4AJR: 3d Structure Of E. Coli Isocitrate Dehydrogenase K100m Mutant In Complex With Alpha-Ketoglutarate, Magnesium(Ii) And Nadph - The Product Complex

NADP(+) dependent isocitrate dehydrogenase (IDH; EC belongs to a large family of alpha-hydroxyacid oxidative beta-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding beta-decarboxylation to an enol intermediate followed by tautomerization to the final alpha-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 beta-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 alpha-hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following beta-decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the alpha-hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism.
PDB ID: 4AJRDownload
MMDB ID: 104487
PDB Deposition Date: 2012/2/17
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.69  Å
Source Organism:
Similar Structures:
Biological Unit for 4AJR: dimeric; determined by author and by software (PISA)
Molecular Components in 4AJR
Label Count Molecule
Proteins (2 molecules)
Isocitrate Dehydrogenase [nadp](Gene symbol: icd)
Molecule annotation
Chemicals (8 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB