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Exploring molecular determinants of polysaccharide lyase family 6–1 enzyme activity

Abstract : Abstract The polysaccharide lyase family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1–3. To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exolyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirms that the conserved residues in subsites −1 to +3 of the catalytic site form a common platform that can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel β-helix fold shared by all these enzymes, the substrate-binding site harbors the same overall conserved structures and organization. Despite this apparent similarity, it appears that members of the PL6_1 subfamily specifically accommodate and catalyze the degradation of different alginates suggesting that this common platform is actually a highly adaptable and specific tool.
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https://hal-cnrs.archives-ouvertes.fr/hal-03379698
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Submitted on : Friday, October 15, 2021 - 10:12:16 AM
Last modification on : Thursday, December 2, 2021 - 2:14:02 PM

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Sébastien Violot, Frédéric Galisson, Loïc Carrique, Vinesh Jugnarain, Léa Conchou, et al.. Exploring molecular determinants of polysaccharide lyase family 6–1 enzyme activity. Glycobiology, Oxford University Press (OUP), 2021, ⟨10.1093/glycob/cwab073⟩. ⟨hal-03379698⟩

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