Structural Analyses of Substrate–pH Activity Pairing Observed across Diverse Polysaccharide Lyases
Structural Analyses of Substrate–pH Activity Pairing Observed across Diverse Polysaccharide Lyases
复制标题
不同多糖裂解酶中观察到的底物与 pH 活性配对的结构分析
DOI：
10.1021/acs.biochem.3c00321
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发表时间：
2023
期刊：
影响因子：
2.9
通讯作者：
Acharya, Rudresh
中科院分区：
文献类型：
--
作者：
Pandey, Shubhant;Berger, Bryan W.;Acharya, Rudresh
自然界中发现的阴离子多糖在功能和结构上是多样的，催化其降解的多糖裂解酶（PLs）也是如此。根据其可裂解的基板结构的各种PL折叠的原子叠加证实了在PL活性位点的结构收敛的发生。这表明在进化过程中出现了各种PL折叠以切割特定类别的阴离子多糖。而PL活性位点的结构和机制的相似性已在早期的研究中被强调，关于这种催化收敛的功能特性的详细理解仍然是一个悬而未决的问题，特别是外在因素如pH在底物结合和催化的背景下的作用。我们早期的结构和功能的Smlt 1473的pH指导多底物特异性的工作启发我们重组PL根据底物类型来分析其催化活性的pH依赖性。有趣的是，我们发现，在特定的pH值范围内（酸性/中性/碱性），无论PL折叠，促进功能收敛的想法，以及特定组的基板被切割。在此观察的基础上，我们着手从结构和计算上定义PL家族中活性位点的关键成分。这项研究描绘了保守的“底物pH活性配对”内和PL家族之间的结构决定因素。
Anionic polysaccharides found in nature are functionally and structurally diverse, and so are the polysaccharide lyases (PLs) that catalyze their degradation. Atomic superposition of various PL folds according to their cleavable substrate structure confirms the occurrence of structural convergence at PL active sites. This suggests that various PL folds have emerged to cleave a particular class of anionic polysaccharide during the course of evolution. Whereas the structural and mechanistic similarity of PL active site has been highlighted in earlier studies, a detailed understanding regarding functional properties of this catalytic convergence remains an open question, especially the role of extrinsic factors such as pH in the context of substrate binding and catalysis. Our earlier structural and functional work on pH directed multisubstrate specificity of Smlt1473 inspired us to regroup PLs according to substrate type to analyze the pH dependence of their catalytic activity. Interestingly, we find that particular groups of substrates are cleaved in a particular pH range (acidic/neutral/basic) irrespective of PL fold, boosting the idea of functional convergence as well. On the basis of this observation, we set out to define structurally and computationally the key constituents of an active site among PL families. This study delineates the structural determinants of conserved “substrate–pH activity pairing” within and between PL families.