The Swiss Army Knife of Alginate Manipulation - A Gut Bacterium Alginate Lyase with Diverse Catalytic Activities

Tandrup, T.; Rivas-Fernandez, J. P.; Madsen, M.; Ronne, M. E.; Petersen, A. B.; Klau, L. J.; Tondervik, A.; Wilkens, C.; Aachmann, F. L.; Rovira, C.; Svensson, B.

doi:10.1101/2024.12.11.627697

bioRxiv · 10.1101/2024.12.11.627697

The Swiss Army Knife of Alginate Manipulation - A Gut Bacterium Alginate Lyase with Diverse Catalytic Activities

Tandrup, T.·Rivas-Fernandez, J. P.·Madsen, M.·Ronne, M. E.·Petersen, A. B.·Klau, L. J.·Tondervik, A.·Wilkens, C.·Aachmann, F. L.·Rovira, C.·Svensson, B.

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Abstract

The alginate-degrading enzyme BoPL38 of the human gut bacterium Bacteroides ovatus CP926 degrades the three polysaccharide structures found in alginate, a major constituent of brown macroalgae with numerous industrial applications. However, the detailed mechanisms of alginate-degrading enzymes remain unclear. Crystal structures of BoPL38 complexes with alginate oligosaccharides, now shed light on the enzymes catalytic machinery. QM/MM simulations reveal distinct conformational and reaction pathways, highlighting different transition states for mannuronate and guluronate conversion. C5 proton abstraction at subsite +1 by Y298 and H243 facilitates syn- and anti-{beta}-elimination reactions, respectively. Substrate recognition relies on R292 distorting the sugar at subsite +1 into a preactivated conformation, while stabilizing the active site tunnel through a salt bridge. Furthermore, NMR spectroscopy found that BoPL38 also catalyze mannuronate to guluronate epimerization in addition to its lyase function, thereby paving the way for future enzymatic alginate modification.

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Tandrup, T., Rivas-Fernandez, J. P., Madsen, M., Ronne, M. E., Petersen, A. B., Klau, L. J., Tondervik, A., Wilkens, C., Aachmann, F. L., Rovira, C., Svensson, B.. 2024-12-11. The Swiss Army Knife of Alginate Manipulation - A Gut Bacterium Alginate Lyase with Diverse Catalytic Activities. https://doi.org/10.1101/2024.12.11.627697

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