Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, CA 94158, USA.
Curr Opin Chem Biol. 2011 Jun;15(3):435-42. doi: 10.1016/j.cbpa.2011.03.008. Epub 2011 Apr 12.
Classification of enzyme function should be quantitative, computationally accessible, and informed by sequences and structures to enable use of genomic information for functional inference and other applications. Large-scale studies have established that divergently evolved enzymes share conserved elements of structure and common mechanistic steps and that convergently evolved enzymes often converge to similar mechanisms too, suggesting that reaction mechanisms could be used to develop finer-grained functional descriptions than provided by the Enzyme Commission (EC) system currently in use. Here we describe how evolution informs these structure-function mappings and review the databases that store mechanisms of enzyme reactions along with recent developments to measure ligand and mechanistic similarities. Together, these provide a foundation for new classifications of enzyme function.
酶功能的分类应该是定量的、可计算的，并通过序列和结构来提供信息，以利用基因组信息进行功能推断和其他应用。大规模的研究已经确立，进化上不同的酶共享结构的保守元素和共同的机制步骤，而进化上趋同的酶通常也趋向于相似的机制，这表明反应机制可以用于比目前使用的酶委员会（EC）系统更精细地描述功能。在这里，我们描述了进化如何提供这些结构-功能映射，并回顾了存储酶反应机制的数据库以及最近用于测量配体和机制相似性的进展。这些共同为酶功能的新分类提供了基础。
