Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis

Nat Chem Biol. 2014 Oct;10(10):823-9. doi: 10.1038/nchembio.1608. Epub 2014 Aug 17.


Despite intensive research, the cyclodehydratase responsible for azoline biogenesis in thiazole/oxazole-modified microcin (TOMM) natural products remains enigmatic. The collaboration of two proteins, C and D, is required for cyclodehydration. The C protein is homologous to E1 ubiquitin-activating enzymes, whereas the D protein is within the YcaO superfamily. Recent studies have demonstrated that TOMM YcaOs phosphorylate amide carbonyl oxygens to facilitate azoline formation. Here we report the X-ray crystal structure of an uncharacterized YcaO from Escherichia coli (Ec-YcaO). Ec-YcaO harbors an unprecedented fold and ATP-binding motif. This motif is conserved among TOMM YcaOs and is required for cyclodehydration. Furthermore, we demonstrate that the C protein regulates substrate binding and catalysis and that the proline-rich C terminus of the D protein is involved in C protein recognition and catalysis. This study identifies the YcaO active site and paves the way for the characterization of the numerous YcaO domains not associated with TOMM biosynthesis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adenosine Triphosphate / chemistry*
  • Adenosine Triphosphate / metabolism
  • Amino Acid Motifs
  • Bacteriocins / chemistry*
  • Bacteriocins / genetics
  • Bacteriocins / metabolism
  • Catalytic Domain
  • Crystallography, X-Ray
  • Escherichia coli / chemistry*
  • Escherichia coli / enzymology
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Hydro-Lyases / chemistry*
  • Hydro-Lyases / genetics
  • Hydro-Lyases / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Oxazoles / chemistry
  • Oxazoles / metabolism
  • Phosphotransferases / chemistry*
  • Phosphotransferases / genetics
  • Phosphotransferases / metabolism
  • Protein Binding
  • Protein Biosynthesis
  • Protein Folding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Thiazoles / chemistry
  • Thiazoles / metabolism
  • Ubiquitin-Activating Enzymes / chemistry*
  • Ubiquitin-Activating Enzymes / genetics
  • Ubiquitin-Activating Enzymes / metabolism


  • Bacteriocins
  • Escherichia coli Proteins
  • Oxazoles
  • Thiazoles
  • microcin
  • Adenosine Triphosphate
  • Phosphotransferases
  • Hydro-Lyases
  • Ubiquitin-Activating Enzymes