Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein

Nat Chem Biol. 2018 Jun;14(6):542-547. doi: 10.1038/s41589-018-0043-2. Epub 2018 Apr 23.

Abstract

The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme-substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations. Our work reveals the molecular evolutionary processes that underlie the emergence of enzymes de novo, which are notably mirrored by recent examples of computational enzyme design and directed evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carrier Proteins
  • Catalysis
  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA Mutational Analysis
  • Escherichia coli / enzymology*
  • Evolution, Molecular
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Mutagenesis
  • Mutation
  • Oligonucleotides / genetics
  • Phylogeny
  • Prephenate Dehydratase / chemistry*
  • Prephenate Dehydratase / genetics*
  • Protein Binding
  • Protein Conformation
  • Spectrometry, Fluorescence
  • Substrate Specificity

Substances

  • Carrier Proteins
  • Oligonucleotides
  • cyclohexadienyl dehydratase
  • Prephenate Dehydratase