8PC3

Crystal structure of Paradendryphiella salina PL7C alginate lyase in complex with pentamannuronic acid

8PC3 の概要

• エントリーDOI: 10.2210/pdb8pc3/pdb
• 関連するPDBエントリー: 8C3X
• 分子名称: Alginate lyase, beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid, beta-D-mannopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid, ... (5 entities in total)
• 機能のキーワード: alginate lyase, complex, beta-jelly roll, lyase
• 由来する生物種: Paradendryphiella salina
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 26778.83

構造登録者

Wilknes, C. (登録日: 2023-06-09, 公開日: 2023-07-12, 最終更新日: 2025-07-02)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.1 Å)