8RBI

Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124

Summary for 8RBI

• Entry DOI: 10.2210/pdb8rbi/pdb
• Descriptor: Alginate lyase, DI(HYDROXYETHYL)ETHER, SODIUM ION, ... (4 entities in total)
• Functional Keywords: alginate lyase, lyase
• Biological source: Paradendryphiella salina
• Total number of polymer chains: 1
• Total formula weight: 25649.31

Authors

Wilkens, C. (deposition date: 2023-12-04, release date: 2024-01-17, Last modification date: 2025-07-02)

Primary citation

Rivas-Fernandez, J.P.,Vuillemin, M.,Pilgaard, B.,Klau, L.J.,Fredslund, F.,Lund-Hanssen, C.,Welner, D.H.,Meyer, A.S.,Morth, J.P.,Meilleur, F.,Aachmann, F.L.,Rovira, C.,Wilkens, C.
Unraveling the molecular mechanism of polysaccharide lyases for efficient alginate degradation.
Nat Commun, 16:2670-2670, 2025

PubMed 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.

PubMed: 40102416
DOI: 10.1038/s41467-025-56754-5

Experimental method

X-RAY DIFFRACTION (0.98 Å)