Structure of Isocitrate Dehydrogenase With Alpha-Ketoglutarate at 2.7-A Resolution: Conformational Changes Induced by Decarboxylation of Isocitrate

Biochemistry. 1993 Sep 14;32(36):9317-22. doi: 10.1021/bi00087a009.

Abstract

The structure of the isocitrate dehydrogenase (IDH) complex with bound alpha-ketoglutarate, Ca2+, and NADPH was solved at 2.7-A resolution. The alpha-ketoglutarate binds in the active site at the same position and orientation as isocitrate, with a difference between the two bound molecules of about 0.8 A. The Ca2+ metal is coordinated by alpha-ketoglutarate, three conserved aspartate residues, and a pair of water molecules. The largest motion in the active site relative to the isocitrate enzyme complex is observed for tyrosine 160, which originally forms a hydrogen bond to the labile carboxyl group of isocitrate and moves to form a new hydrogen bond to Asp 307 in the complex with alpha-ketoglutarate. This triggers a number of significant movements among several short loops and adjoining secondary structural elements in the enzyme, most of which participate in dimer stabilization and formation of the active-site cleft. These rearrangements are similar to the ligand-binding-induced movements observed in globins and insulin and serve as a model for an enzymatic mechanism which involves local shifts of secondary structural elements during turnover, rather than large-scale domain closures or loop transitions induced by substrate binding such as those observed in hexokinase or triosephosphate isomerase.

Publication types

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

MeSH terms

  • Binding Sites
  • Calcium / chemistry
  • Isocitrate Dehydrogenase / chemistry*
  • Isocitrates / chemistry*
  • Ketoglutaric Acids / chemistry*
  • Protein Conformation
  • X-Ray Diffraction

Substances

  • Isocitrates
  • Ketoglutaric Acids
  • isocitric acid
  • Isocitrate Dehydrogenase
  • Calcium