Unraveling the molecular mechanism of polysaccharide lyases for efficient alginate degradation
Alginate lyases (ALs) catalyze the depolymerization of brown macroalgae alginates, widely used naturally occurring polysaccharides. Their molecular reaction mechanism remains elusive due to the lack of catalytically competent Michaelis-Menten-like complex structures. Here, we provide structural snapshots and dissect the mechanism of mannuronan-specific ALs from family 7 polysaccharide lyases (PL7), employing time-resolved NMR, X-ray, neutron crystallography, and QM/MM simulations. We reveal the protonation state of critical active site residues, enabling atomic-level analysis of the reaction coordinate. Our approach reveals an endolytic and asynchronous syn β-elimination reaction, with Tyr serving as both Brønsted base and acid, involving a carbanion-type transition state. This study not only reconciles previous structural and kinetic discrepancies, but also establishes a comprehensive PL reaction mechanism which is most likely applicable across all enzymes of the PL7 family as well as other PL families.
Authors
- Ditte Hededam Welner (ORCID: https://orcid.org/0000-0001-9297-4133)
- Bo Pilgaard (ORCID: https://orcid.org/0000-0002-8697-6041)
- Folmer Fredslund (ORCID: https://orcid.org/0000-0003-0881-1927)
- Flora Meilleur (ORCID: https://orcid.org/0000-0001-9313-8989)
- Jens Preben Morth (ORCID: https://orcid.org/0000-0003-4077-0192)
- Finn L. Aachmann (ORCID: https://orcid.org/0000-0003-1613-4663)
- M. Paul Vuillemin (ORCID: https://orcid.org/0000-0002-1776-7844)
- Anne S. Meyer (ORCID: https://orcid.org/0000-0001-8910-9931)
- Leesa J. Klau (ORCID: https://orcid.org/0000-0003-2482-3880)
- Carme Rovira (ORCID: https://orcid.org/0000-0003-1477-5010)
- Casper Wilkens (ORCID: https://orcid.org/0000-0001-7692-067X)
- José Pablo Rivas-Fernández (ORCID: https://orcid.org/0000-0002-1349-3049)
- Charlotte Lund-Hanssen
Institutions
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Oak Ridge National Laboratory (US)
- North Carolina State University (US)
- SINTEF (NO)
- Novo Nordisk (Denmark) (DK)
- Norwegian University of Science and Technology (NO)
- Novo Nordisk Foundation (DK)
- Instituto de Química Orgánica General (ES)
- SINTEF Industry (NO)
- Universitat de Barcelona (ES)
- Technical University of Denmark (DK)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-03-18
- DOI
- https://doi.org/10.1038/s41467-025-56754-5
- Citations
- 13
- Primary Topic
- Seaweed-derived Bioactive Compounds
- Type
- article
- Field-Weighted Citation Impact
- 29.56
Funders
- Danmarks Frie Forskningsfond
- Norges Forskningsråd
- Novo Nordisk Fonden
- Agència de Gestió d'Ajuts Universitaris i de Recerca