Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures
Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures
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DOI：
10.1007/s002399910005
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发表时间：
2000-01-01
影响因子：
3.9
通讯作者：
Bujnicki, JM
中科院分区：
文献类型：
--
作者：
Bujnicki, JM
迄今为止，所有试图从多重序列比对中推导出限制性内切核酸酶（ENases）之间的亲缘关系的尝试都受到这些酶的极端分歧的限制。基于约翰逊等人（1990）的方法，我第一次报告了从结构特征酶的原子坐标的定量比较中推断的ENase样蛋白超家族的进化树。所呈现的结果与之前通过晶体学分析获得的比较一致。结果表明，X-外切核酸酶最初从共同祖先分化，然后分支出两个“内切核酸”家族，将“平端切割器”与“5'四碱基突出切割器”分开。“这些数据可能有助于更好地理解ENases，并鼓励使用基于结构的方法来推断极端不同蛋白质之间的系统发育关系。此外，三维结构的比较提供了一个平台，进一步聚类分析的序列相似性之间的不同分支的这个大的蛋白质家族，同源性建模模板的合理选择，和蛋白质工程的目标。
To date all attempts to derive a phyletic relationship among restriction endonucleases (ENases) from multiple sequence alignments have been limited by extreme divergence of these enzymes. Based on the approach of Johnson et al. (1990), I report for the first time the evolutionary tree of the ENase-like protein superfamily inferred from quantitative comparison of atomic coordinates of structurally characterized enzymes. The results presented are in harmony with previous comparisons obtained by crystallographic analyses. It is shown that X-exonuclease initially diverged from the common ancestor and then two "endonucleolytic" families branched out, separating "blunt end cutters" from "5' four-base overhang cutters." These data may contribute to a better understanding of ENases and encourage the use of structure-based methods for inference of phylogenetic relationship among extremely divergent proteins. In addition, the comparison of three-dimensional structures of ENase-like domains provides a platform for further clustering analyses of sequence similarities among different branches of this large protein family, rational choice of homology modeling templates, and targets for protein engineering.