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Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies

机译：酶超家族催化机理及其机理进化的大规模分析

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Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes. (C) 2015 The Authors. Published by Elsevier Ltd.
机译：酶作为生物催化剂，构成所有生命形式的基础。这些蛋白质如何进化其功能仍然是生物学中的一个基本问题。超过100年的详细生物化学研究，再加上现在可获得的大量序列和蛋白质结构数据，意味着我们能够进行大规模分析以解决这个问题。使用一系列计算工具和资源，我们已经汇编了379个结构定义的蛋白质结构域超家族中酶功能的所有实验注释信息，并将进化过程中观察到的功能变化与反应化学变化联系在一起。许多超家族在某种程度上显示出功能上的变化，尽管一种功能通常主导着一个超家族。我们使用定量化学反应变化的方法来揭示进化过程中发生的各种化学变化，并通过详细的例子加以说明。此外，我们使用酶活性位点的结构信息来检查不同的超家族在进化过程中如何改变其催化机制。一些超家族改变了它们进行的反应，而没有改变催化机理。在另一些方面，就催化化学的显着变化而言，就整体化学和底物特异性而言，酶的功能发生了巨大变化。有趣的是，在某些超家族中，亲戚执行相似的功能，但催化机制不同。该分析突出了整个超家族中功能进化的特征，提供了有助于预测未表征序列的功能和设计新的合成酶的见识。 （C）2015作者。由Elsevier Ltd.发布

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