Crystal structure of the C67A mutant of isopentenyl diphosphate isomerase complexed with a mechanism-based irreversible inhibitor

Proteins. 2004 Feb 1;54(2):216-21. doi: 10.1002/prot.10573.

Abstract

Isopentenyl diphosphate:dimethylallyl diphosphate (IPP:DMAPP) isomerase is a key enzyme in the biosynthesis of isoprenoids. The mechanism of the isomerization reaction involves protonation of the unactivated carbon-carbon double bond in the substrate. Analysis of the 1.97 A crystal structure of the inactive C67A mutant of E. coli isopentenyl diphosphate:dimethylallyl diphosphate isomerase complexed with the mechanism-based inactivator 3,4-epoxy-3-methyl-1-butyl diphosphate is in agreement with an isomerization mechanism involving Glu 116, Tyr 104, and Cys 67. In particular, the results are consistent with a mechanism where Glu116 is involved in the protonation step and Cys67 in the elimination step.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Carbon-Carbon Double Bond Isomerases / antagonists & inhibitors*
  • Carbon-Carbon Double Bond Isomerases / chemistry*
  • Carbon-Carbon Double Bond Isomerases / genetics
  • Carbon-Carbon Double Bond Isomerases / metabolism
  • Crystallography, X-Ray
  • Enzyme Inhibitors / chemistry*
  • Enzyme Inhibitors / metabolism*
  • Enzyme Inhibitors / pharmacology
  • Epoxy Compounds / chemistry
  • Epoxy Compounds / metabolism
  • Epoxy Compounds / pharmacology
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Hemiterpenes
  • Isomerism
  • Organophosphorus Compounds / chemistry
  • Organophosphorus Compounds / metabolism
  • Organophosphorus Compounds / pharmacology
  • Point Mutation / genetics*
  • Protons

Substances

  • Enzyme Inhibitors
  • Epoxy Compounds
  • Hemiterpenes
  • Organophosphorus Compounds
  • Protons
  • 3-methyl-3,4-epoxybutyl diphosphate
  • Carbon-Carbon Double Bond Isomerases
  • isopentenyldiphosphate delta-isomerase