Molecular basis for the diversification of lincosamide biosynthesis by pyridoxal phosphate-dependent enzymes
The biosynthesis of the lincosamide antibiotics lincomycin A and celesticetin involves the pyridoxal-5'-phosphate (PLP)-dependent enzymes LmbF and CcbF, which are responsible for bifurcation of the biosynthetic pathways. Despite recognizing the same S-glycosyl-L-cysteine structure of the substrates, LmbF catalyses thiol formation through β-elimination, whereas CcbF produces S-acetaldehyde through decarboxylation-coupled oxidative deamination. The structural basis for the diversification mechanism remains largely unexplored. Here we conduct structure-function analyses of LmbF and CcbF. X-ray crystal structures, docking and molecular dynamics simulations reveal that active-site aromatic residues play important roles in controlling the substrate binding mode and the reaction outcome. Furthermore, the reaction selectivity and oxygen-utilization of LmbF and CcbF were rationally engineered through structure- and calculation-based mutagenesis. Thus, the catalytic function of CcbF was switched to that of LmbF, and, remarkably, both LmbF and CcbF variants gained the oxidative-amidation activity to produce an unnatural S-acetamide derivative of lincosamide.
Authors
- Markéta Koběrská (ORCID: https://orcid.org/0000-0002-9787-4227)
- Takahiro Mori (ORCID: https://orcid.org/0000-0002-2754-5858)
- Zdeněk Kameník (ORCID: https://orcid.org/0000-0002-5363-0597)
- Jiřı́ Janata (ORCID: https://orcid.org/0000-0002-4582-2062)
- Shuang Lyu (ORCID: https://orcid.org/0009-0001-8082-3458)
- Stanislav Kadlčík (ORCID: https://orcid.org/0000-0001-8989-7157)
- Ikuro Abe (ORCID: https://orcid.org/0000-0002-3640-888X)
- Tohru Terada (ORCID: https://orcid.org/0000-0002-7091-0646)
- Kosuke Sakurada
- Yoshitaka Moriwaki (ORCID: https://orcid.org/0000-0003-0448-9790)
- Aninda Mazumdar (ORCID: https://orcid.org/0000-0002-4985-7115)
Institutions
- Czech Academy of Sciences (CZ)
- Japan Science and Technology Agency (JP)
- Institute of Microbiology (BY)
- Innovative Research (United States) (US)
- Czech Academy of Sciences, Institute of Microbiology (CZ)
- Medical Governance Research Institute (JP)
- Innovative Research (United States) (US)
- The University of Tokyo (JP)
Publication Details
- Journal
- Nature Chemistry
- Published
- 2024-12-06
- DOI
- https://doi.org/10.1038/s41557-024-01687-7
- Citations
- 4
- Primary Topic
- Microbial Natural Products and Biosynthesis
- Type
- article
- Field-Weighted Citation Impact
- 1.79
Funders
- Japan Agency for Medical Research and Development
- Japan Society for the Promotion of Science London
- European Commission
- Ministry of Education, Culture, Sports, Science and Technology
- Ministerstvo Školství, Mládeže a Tělovýchovy
- Grantová Agentura České Republiky
- Akademie Věd České Republiky
- Daiichi Sankyo Foundation of Life Science
- Japan Society for the Promotion of Science
- Japan Science and Technology Agency
- RIKEN
- Precursory Research for Embryonic Science and Technology
- Daiichi Sankyo Europe