8PC3
Crystal structure of Paradendryphiella salina PL7C alginate lyase in complex with pentamannuronic acid
Summary for 8PC3
| Entry DOI | 10.2210/pdb8pc3/pdb |
| Related | 8C3X |
| Descriptor | 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) |
| Functional Keywords | alginate lyase, complex, beta-jelly roll, lyase |
| Biological source | Paradendryphiella salina |
| Total number of polymer chains | 1 |
| Total formula weight | 26778.83 |
| Authors | Wilknes, C. (deposition date: 2023-06-09, release date: 2023-07-12, 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 Cited by 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: 40102416DOI: 10.1038/s41467-025-56754-5 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.1 Å) |
Structure validation
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