Structural basis of the mechanism and inhibition of a human ceramide synthase
Ceramides are bioactive sphingolipids crucial for regulating cellular metabolism. Ceramides and dihydroceramides are synthesized by six ceramide synthase (CerS) enzymes, each with specificity for different acyl-CoA substrates. Ceramide with a 16-carbon acyl chain (C16 ceramide) has been implicated in obesity, insulin resistance and liver disease and the C16 ceramide-synthesizing CerS6 is regarded as an attractive drug target for obesity-associated disease. Despite their importance, the molecular mechanism underlying ceramide synthesis by CerS enzymes remains poorly understood. Here we report cryo-electron microscopy structures of human CerS6, capturing covalent intermediate and product-bound states. These structures, along with biochemical characterization, reveal that CerS catalysis proceeds through a ping-pong reaction mechanism involving a covalent acyl-enzyme intermediate. Notably, the product-bound structure was obtained upon reaction with the mycotoxin fumonisin B1, yielding insights into its inhibition of CerS. These results provide a framework for understanding CerS function, selectivity and inhibition and open routes for future drug discovery.
Authors
- Tomas C. Pascoa (ORCID: https://orcid.org/0000-0003-3375-4207)
- A.C.W. Pike (ORCID: https://orcid.org/0000-0001-9661-2607)
- Alexander Pautsch (ORCID: https://orcid.org/0000-0003-0405-6063)
- Gamma Chi (ORCID: https://orcid.org/0000-0001-9910-0965)
- Saša Štefanić (ORCID: https://orcid.org/0000-0001-7367-1831)
- Gisela Schnapp (ORCID: https://orcid.org/0000-0002-1529-0130)
- Sven Thamm (ORCID: https://orcid.org/0000-0002-8799-1155)
- Christofer S. Tautermann (ORCID: https://orcid.org/0000-0002-6935-6940)
- David B. Sauer (ORCID: https://orcid.org/0000-0001-9291-4640)
- Andrew Quigley (ORCID: https://orcid.org/0000-0002-5022-9845)
- R. Chalk (ORCID: https://orcid.org/0000-0002-9942-2339)
- Elisabeth P. Carpenter
- Michael Traub
Institutions
- Boehringer Ingelheim (Germany) (DE)
- ZHAW Zurich University of Applied Sciences (CH)
- University of Zurich (CH)
- Nuffield Orthopaedic Centre (GB)
- Diamond Light Source (GB)
- University of Oxford (GB)
- Oxford BioMedica (United Kingdom) (GB)
Publication Details
- Journal
- Nature Structural & Molecular Biology
- Published
- 2024-11-11
- DOI
- https://doi.org/10.1038/s41594-024-01414-3
- Citations
- 14
- Primary Topic
- Sphingolipid Metabolism and Signaling
- Type
- article
- Field-Weighted Citation Impact
- 3.27
Funders
- Pfizer
- McGill University
- Genome Canada
- Wellcome Trust
- Diamond Light Source
- European Federation of Pharmaceutical Industries and Associations
- Ontario Ministry of Economic Development and Innovation
- European Commission
- Medical Research Council Canada
- Ministero dello Sviluppo Economico
- Medical Research Council