Design and evolution of an enzyme with a non-canonical organocatalytic mechanism

Nature. 2019 Jun;570(7760):219-223. doi: 10.1038/s41586-019-1262-8. Epub 2019 May 27.

Abstract

The combination of computational design and laboratory evolution is a powerful and potentially versatile strategy for the development of enzymes with new functions1-4. However, the limited functionality presented by the genetic code restricts the range of catalytic mechanisms that are accessible in designed active sites. Inspired by mechanistic strategies from small-molecule organocatalysis5, here we report the generation of a hydrolytic enzyme that uses Nδ-methylhistidine as a non-canonical catalytic nucleophile. Histidine methylation is essential for catalytic function because it prevents the formation of unreactive acyl-enzyme intermediates, which has been a long-standing challenge when using canonical nucleophiles in enzyme design6-10. Enzyme performance was optimized using directed evolution protocols adapted to an expanded genetic code, affording a biocatalyst capable of accelerating ester hydrolysis with greater than 9,000-fold increased efficiency over free Nδ-methylhistidine in solution. Crystallographic snapshots along the evolutionary trajectory highlight the catalytic devices that are responsible for this increase in efficiency. Nδ-methylhistidine can be considered to be a genetically encodable surrogate of the widely employed nucleophilic catalyst dimethylaminopyridine11, and its use will create opportunities to design and engineer enzymes for a wealth of valuable chemical transformations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 4-Aminopyridine / analogs & derivatives
  • 4-Aminopyridine / metabolism
  • Biocatalysis
  • Catalytic Domain / genetics
  • Crystallography, X-Ray
  • Directed Molecular Evolution*
  • Esters / metabolism
  • Genetic Code
  • Hydrolases / chemistry
  • Hydrolases / genetics*
  • Hydrolases / metabolism*
  • Hydrolysis
  • Methylhistidines / metabolism
  • Models, Molecular
  • Mutagenesis
  • Mutation
  • Protein Engineering*
  • Pyrococcus horikoshii / enzymology
  • Pyrococcus horikoshii / genetics
  • Substrate Specificity / genetics

Substances

  • Esters
  • Methylhistidines
  • 4-Aminopyridine
  • Hydrolases
  • 2-haloacid dehalogenase
  • 4-dimethylaminopyridine