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.

中文翻译：

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探索多糖裂解酶家族 6-1 酶活性的分子决定因素

摘要

多糖裂解酶家族 6 (PL6) 代表 CAZy 数据库中分类的 41 个多糖裂解酶家族之一，其绝大多数成员是藻酸盐裂解酶，分为三个亚家族 PL6_1-3。为了破译属于亚家族 PL6_1 的酶的识别和作用方式，我们解析了 Pedsa0632、Patl3640、Pedsa3628 和 Pedsa3807 的晶体结构，它们都显示出不同的底物特异性和作用方式（内切酶/外切酶）。彻底探索 Pedsa0632 和 Patl3640 与其底物复合的结构以及对接实验证实，催化位点 -1 至 +3 亚位点中的保守残基形成了一个通用平台，可以以非常相似的方式容纳各种类型的海藻酸盐方式，但通过一系列原创改编，为他们带来了行动的特殊性。通过与 PL6_1 藻酸盐裂解酶现有结构的比较研究，我们观察到在所有这些酶共享的右手平行 β-螺旋折叠中，底物结合位点具有相同的整体保守结构和组织。尽管有这种明显的相似之处，