Ground state destabilization from a positioned general base in the ketosteroid isomerase active site

Biochemistry. 2013 Feb 12;52(6):1074-81. doi: 10.1021/bi301348x. Epub 2013 Jan 30.


We compared the binding affinities of ground state analogues for bacterial ketosteroid isomerase (KSI) with a wild-type anionic Asp general base and with uncharged Asn and Ala in the general base position to provide a measure of potential ground state destabilization that could arise from the close juxtaposition of the anionic Asp and hydrophobic steroid in the reaction's Michaelis complex. The analogue binding affinity increased ~1 order of magnitude for the Asp38Asn mutation and ~2 orders of magnitude for the Asp38Ala mutation, relative to the affinity with Asp38, for KSI from two sources. The increased level of binding suggests that the abutment of a charged general base and a hydrophobic steroid is modestly destabilizing, relative to a standard state in water, and that this destabilization is relieved in the transition state and intermediate in which the charge on the general base has been neutralized because of proton abstraction. Stronger binding also arose from mutation of Pro39, the residue adjacent to the Asp general base, consistent with an ability of the Asp general base to now reorient to avoid the destabilizing interaction. Consistent with this model, the Pro mutants reduced or eliminated the increased level of binding upon replacement of Asp38 with Asn or Ala. These results, supported by additional structural observations, suggest that ground state destabilization from the negatively charged Asp38 general base provides a modest contribution to KSI catalysis. They also provide a clear illustration of the well-recognized concept that enzymes evolve for catalytic function and not, in general, to maximize ground state binding. This ground state destabilization mechanism may be common to the many enzymes with anionic side chains that deprotonate carbon acids.

Publication types

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

MeSH terms

  • Alanine / chemistry
  • Alanine / genetics
  • Alanine / metabolism*
  • Asparagine / chemistry
  • Asparagine / genetics
  • Asparagine / metabolism*
  • Aspartic Acid / chemistry
  • Aspartic Acid / genetics
  • Aspartic Acid / metabolism*
  • Binding Sites
  • Catalysis
  • Catalytic Domain
  • Comamonas testosteroni / enzymology*
  • Comamonas testosteroni / genetics
  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Ketosteroids / metabolism
  • Kinetics
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Mutation / genetics
  • Pseudomonas putida / enzymology*
  • Pseudomonas putida / genetics
  • Steroid Isomerases / chemistry*
  • Steroid Isomerases / genetics
  • Steroid Isomerases / metabolism


  • Ketosteroids
  • Aspartic Acid
  • Asparagine
  • Steroid Isomerases
  • Alanine