The bottromycin epimerase BotH defines a group of atypical α/β-hydrolase-fold enzymes

Nat Chem Biol. 2020 Sep;16(9):1013-1018. doi: 10.1038/s41589-020-0569-y. Epub 2020 Jun 29.

Abstract

D-amino acids endow peptides with diverse, desirable properties, but the post-translational and site-specific epimerization of L-amino acids into their D-counterparts is rare and chemically challenging. Bottromycins are ribosomally synthesized and post-translationally modified peptides that have overcome this challenge and feature a D-aspartate (D-Asp), which was proposed to arise spontaneously during biosynthesis. We have identified the highly unusual α/β-hydrolase (ABH) fold enzyme BotH as a peptide epimerase responsible for the post-translational epimerization of L-Asp to D-Asp during bottromycin biosynthesis. The biochemical characterization of BotH combined with the structures of BotH and the BotH-substrate complex allowed us to propose a mechanism for this reaction. Bioinformatic analyses of BotH homologs show that similar ABH enzymes are found in diverse biosynthetic gene clusters. This places BotH as the founding member of a group of atypical ABH enzymes that may be able to epimerize non-Asp stereocenters across different families of secondary metabolites.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aspartic Acid / chemistry
  • Aspartic Acid / metabolism
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Crystallography, X-Ray
  • Evolution, Molecular
  • Models, Molecular
  • Multigene Family
  • Peptides, Cyclic / metabolism
  • Protein Conformation
  • Protein Folding
  • Racemases and Epimerases / chemistry*
  • Racemases and Epimerases / genetics
  • Racemases and Epimerases / metabolism*
  • Streptomyces / enzymology
  • Streptomyces / genetics
  • Substrate Specificity

Substances

  • Bacterial Proteins
  • Peptides, Cyclic
  • bottromycin
  • Aspartic Acid
  • Racemases and Epimerases