Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily
Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily
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DOI：
10.1016/j.jmb.2006.04.055
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发表时间：
2006-06-30
影响因子：
5.6
通讯作者：
Babbitt, Patricia C.
中科院分区：
文献类型：
--
作者：
Glasner, Margaret E.;Fayazmanesh, Nima;Babbitt, Patricia C.
了解蛋白质如何进化以提供精致的特异性和熟练的活性是生物学中的一个基本问题，对蛋白质功能预测和蛋白质工程具有影响。为了研究这个问题，我们分析了结构和功能的进化o-琥珀酰苯甲酸合酶/N-酰基氨基酸消旋酶（OSBS/NAAAR）的家庭，一部分的机械多样性烯醇化酶超家族。尽管该家族的所有特征性成员都催化OSBS反应，但该家族非常不同，其中一些成员共享< 15%的同一性。此外，该家族的一个成员，拟无枝酸菌OSBS/NAAAR，是混杂的，催化脱水和外消旋。虽然OSBS/NAAAR家族似乎有一个单一的进化起源，没有序列或结构基序独特的这个家庭可以被确定，在家庭中保守的所有残基也被发现在烯醇化酶超家族成员，具有不同的功能。基于它们的物种分布，几个未知的蛋白质类似Amycolatopsis OSBS/NAAAR似乎已经通过横向基因转移。像拟无枝酸菌OSBS/NAAAR一样，这些可能具有OSBS的额外或替代功能，因为许多来自缺乏OSBS作为中间体的途径的生物体。除了功能差异外，OSBS/NAAAR家族还表现出令人惊讶的结构变化，包括两个结构域之间的方向差异。这些结果为蛋白质进化提供了一些见解。首先，正向同源蛋白可以表现出显著的结构变异，并且可以在配体接触残基几乎不保守的情况下保持特异性。其次，一组类似于拟无枝酸菌OSBS/NAAAR的蛋白质的发现支持了新的蛋白质功能通过混杂中间体进化的假设。最后，结合进化，结构和序列分析确定的特征，可能总理蛋白质，如Amycolatopsis OSBS/NAAAR，为新的活动的演变。(c)2006爱思唯尔有限公司保留所有权利。
Understanding how proteins evolve to provide both exquisite specificity and proficient activity is a fundamental problem in biology that has implications for protein function prediction and protein engineering. To study this problem, we analyzed the evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase (OSBS/NAAAR) family, part of the mechanistically diverse enolase superfamily. Although all characterized members of the family catalyze the OSBS reaction, this family is extraordinarily divergent, with some members sharing < 15% identity. In addition, a member of this family, Amycolatopsis OSBS/NAAAR, is promiscuous, catalyzing both dehydration and racemization. Although the OSBS/NAAAR family appears to have a single evolutionary origin, no sequence or structural motifs unique to this family could be identified; all residues conserved in the family are also found in enolase superfamily members that have different functions. Based on their species distribution, several uncharacterized proteins similar to Amycolatopsis OSBS/NAAAR appear to have been transmitted by lateral gene transfer. Like Amycolatopsis OSBS/NAAAR, these might have additional or alternative functions to OSBS because many are from organisms lacking the pathway in which OSBS is an intermediate. In addition to functional differences, the OSBS/NAAAR family exhibits surprising structural variations, including large differences in orientation between the two domains. These results offer several insights into protein evolution. First, orthologous proteins can exhibit significant structural variation, and specificity can be maintained with little conservation of ligand-contacting residues. Second, the discovery of a set of proteins similar to Amycolatopsis OSBS/NAAAR supports the hypothesis that new protein functions evolve through promiscuous intermediates. Finally, a combination of evolutionary, structural, and sequence analyses identified characteristics that might prime proteins, such as Amycolatopsis OSBS/NAAAR, for the evolution of new activities. (c) 2006 Elsevier Ltd. All rights reserved.