Elucidation of the catalytic mechanism of an enzyme that transfers a coenzyme backbone

September 12, 2025

A step toward customizing antibiotics using enzymes

Natural products continue to serve as important resources for pharmaceuticals, but the number of new compounds provided by classical methods has been declining, and new approaches are needed. In this study, the researchers at the RIKEN CSRS focused on the enzyme NAT, which transfers the 3-amino-3-carboxypropyl (3-ACP) donor from S-adenosylmethionine (SAM) during β-lactam antibiotic biosynthesis. Through X-ray crystallography, they revealed the structural basis of substrate recognition. By integrating site-directed mutagenesis, thermal denaturation analysis, molecular dynamics simulations, and QM/MM calculations, the team tracked the 3-ACP transfer reaction at the atomic level. The results showed that the amino group of SAM functions as a Brønsted base, enhancing the nucleophilicity of the substrate and thereby promoting a nucleophilic substitution reaction at the Cγ methylene of SAM. This study presents a comprehensive structural, biophysical, and computational framework for understanding 3-ACP transfer and offers a catalytic mechanism for the biosynthesis of novel β-lactam antibiotic scaffolds. This research is expected to contribute to the production of valuable compounds through enzyme engineering and synthetic biology.

 

Original article

Journal of the American Chemical Society　doi: 10.1021/jacs.5c08367

Y. Gao, M. Karasawa, Z. Quan, T. Mori, M. Kanaida, C. A. Townsend, T. Terada, I. Abe, T. Awakawa,

"Structural basis for 3-amino-3-carboxypropyl transfer in nocardicin biosynthesis".

Contact

Takayoshi Awakawa
Team Director
Chemical Biology and Biosynthesis Research Team