Structure of Thermus thermophilus type 2 isopentenyl diphosphate isomerase inferred from crystallography and molecular dynamics

Biochem Biophys Res Commun. 2005 Dec 23;338(3):1515-8. doi: 10.1016/j.bbrc.2005.10.114. Epub 2005 Oct 27.

Abstract

Crystal structures of Thermus thermophilus and Bacillus subtilis type 2 IPP isomerases were combined to generate an almost complete model of the FMN-bound structure of the enzyme. In contrast to previous studies, positions of flexible loops were obtained and carefully analyzed by molecular dynamics. Docking simulations find a unique putative binding site for the IPP substrate.

Publication types

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

MeSH terms

  • Carbon-Carbon Double Bond Isomerases / chemistry*
  • Carbon-Carbon Double Bond Isomerases / metabolism*
  • Catalysis
  • Crystallography, X-Ray
  • Hemiterpenes / chemistry
  • Hemiterpenes / metabolism
  • Models, Molecular
  • Organophosphorus Compounds / chemistry
  • Organophosphorus Compounds / metabolism
  • Protein Structure, Quaternary
  • Thermus thermophilus / enzymology*

Substances

  • Hemiterpenes
  • Organophosphorus Compounds
  • isopentenyl pyrophosphate
  • Carbon-Carbon Double Bond Isomerases
  • isopentenyldiphosphate delta-isomerase