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This study reveals the first structure of a YcaO enzyme with its peptide substrate, clarifying thioamide formation mechanisms. This work advances understanding of YcaO enzymes and their roles in ribosomally synthesized and post-translationally modified peptides (RiPPs).

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Area of Science:

  • Biochemistry and Structural Biology
  • Enzymology
  • Bioorganic Chemistry

Background:

  • YcaO enzymes catalyze crucial peptide modifications like azoline heterocycle and thioamide formation.
  • These enzymes are integral to the biosynthesis of various ribosomally synthesized and post-translationally modified peptides (RiPPs).
  • Significant knowledge gaps exist regarding the precise mechanisms and structures governing YcaO-mediated reactions.

Purpose of the Study:

  • To present the first atomic-level structure of a YcaO enzyme complexed with its peptide substrate.
  • To elucidate the structural and mechanistic basis of thioamide formation by the YcaO enzyme from *Methanocaldococcus jannaschii*.
  • To explore the functional versatility and evolutionary history of the YcaO enzyme family.

Main Methods:

  • X-ray crystallography to determine the structure of the YcaO-peptide substrate complex.
  • Site-directed mutagenesis to identify key residues for substrate binding and catalysis.
  • Bioinformatic analysis to survey YcaO enzyme diversity and evolutionary relationships.

Main Results:

  • The first structure of a YcaO enzyme bound to its peptide substrate in the active site was determined.
  • Key residues involved in substrate recognition and catalytic activity were identified and validated through mutagenesis.
  • Thioamide-forming YcaO enzymes demonstrated the ability to perform cyclodehydration, indicating conserved mechanisms within the YcaO family.

Conclusions:

  • The presented structural and mechanistic data provide a molecular framework for understanding YcaO enzymes and their role in RiPP biosynthesis.
  • This work reconciles previous findings on RiPP cyclodehydratases and offers insights into azoline-forming YcaO enzymes.
  • The findings lay the groundwork for understanding additional RiPP biosynthetic pathways and enzyme functions.