TY - JOUR
T1 - Unraveling the molecular mechanism of polysaccharide lyases for efficient alginate degradation
AU - Rivas-Fernández, José Pablo
AU - Vuillemin, Marlene
AU - Pilgaard, Bo
AU - Klau, Leesa J.
AU - Fredslund, Folmer
AU - Lund-Hanssen, Charlotte
AU - Welner, Ditte H.
AU - Meyer, Anne S.
AU - Morth, J. Preben
AU - Meilleur, Flora
AU - Aachmann, Finn L.
AU - Rovira, Carme
AU - Wilkens, Casper
PY - 2025
Y1 - 2025
N2 - 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.
AB - 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.
U2 - 10.1038/s41467-025-56754-5
DO - 10.1038/s41467-025-56754-5
M3 - Journal article
C2 - 40102416
SN - 2041-1723
VL - 16
JO - Nature Communications
JF - Nature Communications
M1 - 2670
ER -