Journal Article

PUBDB-2025-01425

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Unraveling the molecular mechanism of polysaccharide lyases for efficient alginate degradation

Rivas-Fernández, J. P. ; Vuillemin, M. ; Pilgaard, B. ; Klau, L. J. ; Fredslund, F. ; Lund-Hanssen, C. ; Welner, D. H. ; Meyer, A. S. ; Morth, J. P.Extern*EMBL* ; Meilleur, F. ; Aachmann, F. L. ; Rovira, C. (Corresponding author) ; Wilkens, C. (Corresponding author)Extern*EMBL*

2025
Springer Nature [London]

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Please use a persistent id in citations: doi:10.1038/s41467-025-56754-5  doi:10.3204/PUBDB-2025-01425

Abstract: 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.

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Contributing Institute(s):

1. EMBL-User (EMBL-User)

Research Program(s):

1. 6G3 - PETRA III (DESY) (POF4-6G3) (POF4-6G3)

Experiment(s):

1. PETRA Beamline P13 (PETRA III)
2. PETRA Beamline P14 (PETRA III)

Appears in the scientific report 2025

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