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Peptide Epimerization Machineries Found in Microorganisms.

Yasushi Ogasawara1, Tohru Dairi1

  • 1Graduate School of Engineering, Hokkaido University, Sapporo, Japan.

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|February 23, 2018
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Summary

This study reviews peptide epimerization enzymes that introduce D-amino acids into peptides. It covers enzymes involved in bacterial peptidoglycan biosynthesis and secondary metabolite production, including NRPS, lantibiotics, and rSAM enzymes.

Keywords:
D-amino acidbiosynthesisepimerasemicroorganismnatural productspeptidepeptidoglycan

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Area of Science:

  • Biochemistry
  • Microbiology
  • Enzymology

Background:

  • D-amino acid residues are found in peptides across eukaryotes and prokaryotes.
  • In microorganisms, UDP-N-acetylmuramic acid pentapeptide is a key unit of peptidoglycan, typically synthesized using racemases.
  • Recent discoveries include unique unidirectional epimerases, expanding the known mechanisms for D-amino acid incorporation.

Purpose of the Study:

  • To review the discovery and mechanistic understanding of peptide epimerization enzymes.
  • To highlight enzymes involved in both primary metabolism (peptidoglycan biosynthesis) and secondary metabolite production.
  • To provide an overview of different enzymatic machineries responsible for introducing D-amino acid residues into peptides.

Main Methods:

  • Literature review of published studies on peptide epimerization enzymes.
  • Analysis of known biosynthetic pathways for peptidoglycans and microbial peptides.
  • Examination of enzymatic mechanisms, including those of non-ribosomal peptide synthetases (NRPS), lantibiotic biosynthesis enzymes, and radical-S-adenosylmethionine (rSAM) enzymes.

Main Results:

  • Identified a unique unidirectional L-Glu epimerase in UDP-MurNAc-L-Ala-L-Glu metabolism.
  • Described three distinct peptide epimerization machineries in secondary metabolite biosynthesis: NRPS, lantibiotic enzymes, and rSAM-dependent enzymes.
  • Clarified mechanisms for D-amino acid formation, including epimerization, dehydration-rehydration, and reduction pathways.

Conclusions:

  • Peptide epimerization is achieved through diverse enzymatic mechanisms in microorganisms.
  • Understanding these enzymes is crucial for elucidating the biosynthesis of various bioactive peptides.
  • Further research into these machineries can inform the prediction and engineering of novel peptide structures.