Induced fit and the catalytic mechanism of isocitrate dehydrogenase

Biochemistry. 2012 Sep 11;51(36):7098-115. doi: 10.1021/bi300483w. Epub 2012 Aug 27.


NADP(+) dependent isocitrate dehydrogenase (IDH; EC 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenine Nucleotides / metabolism
  • Adenine Nucleotides / pharmacology
  • Biocatalysis*
  • Catalytic Domain / drug effects*
  • Escherichia coli / enzymology
  • Isocitrate Dehydrogenase / chemistry*
  • Isocitrate Dehydrogenase / metabolism*
  • Models, Molecular
  • NADP / metabolism
  • NADP / pharmacology
  • Nicotinamide Mononucleotide / metabolism
  • Nicotinamide Mononucleotide / pharmacology


  • Adenine Nucleotides
  • Nicotinamide Mononucleotide
  • NADP
  • Isocitrate Dehydrogenase

Associated data

  • PDB/4AJ3
  • PDB/4AJA
  • PDB/4AJB
  • PDB/4AJC
  • PDB/4AJR
  • PDB/4AJS
  • PDB/X1
  • PDB/X2