酶已经通过数十亿年的进化形成,以催化支持地球上生命的化学反应。分散在文献中,或组织在在线数据库中,关于酶的知识可以在不同的维度上构建,要么与它们作为生物大分子的质量有关,比如它们的序列和结构,或者与它们的化学功能有关,如催化位点,动力学,机制,整体反应。只有考虑到这些维度中的每一个,才能理解酶的进化。此外,酶的许多特性只有在进化的光下才有意义。我们从概述酶进化的主要范例开始这篇综述,包括基因复制和分化,趋同进化,和通过结构域重组进行进化。在第二部分,我们概述了当前关于酶的集体知识,由不同类型的数据组织并收集在几个数据库中。我们还强调了一些越来越强大的计算工具,这些工具可以用来缩小理解方面的差距,特别是对于需要费力的实验方案的数据类型。我们认为,蛋白质结构预测的最新进展将是预测结合的有力催化剂,机制,最终,化学反应。在不久的将来,可能会实现酶功能和进化的全面映射。
Enzymes have been shaped by evolution over billions of years to catalyse the chemical reactions that support life on earth. Dispersed in the literature, or organised in online databases, knowledge about enzymes can be structured in distinct dimensions, either related to their quality as biological macromolecules, such as their sequence and structure, or related to their chemical functions, such as the catalytic site, kinetics, mechanism, and overall reaction. The evolution of enzymes can only be understood when each of these dimensions is considered. In addition, many of the properties of enzymes only make sense in the light of evolution. We start this review by outlining the main paradigms of enzyme evolution, including gene duplication and divergence, convergent evolution, and evolution by recombination of domains. In the second part, we overview the current collective knowledge about enzymes, as organised by different types of data and collected in several databases. We also highlight some increasingly powerful computational tools that can be used to close gaps in understanding, in particular for types of data that require laborious experimental protocols. We believe that recent advances in protein structure prediction will be a powerful catalyst for the prediction of binding, mechanism, and ultimately, chemical reactions. A comprehensive mapping of enzyme function and evolution may be attainable in the near future.