The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: Insight from molecular modeling and phylogenetic analysis
The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: Insight from molecular modeling and phylogenetic analysis
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DOI：
10.1023/a:1008131810233
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发表时间：
2001-03-01
期刊：
影响因子：
1.6
通讯作者：
Rychlewski, L
中科院分区：
文献类型：
--
作者：
Bujnicki, JM;Rychlewski, L
PD-(D/E)XK超家族脱氧核糖核酸酶包括限制性内切酶、核酸外切酶和刻痕酶，它们具有共同的折叠和活性部位的结构。它们的极端分歧通常阻碍了仅基于序列比较的新成员的识别。在这里，我们报告了噬菌体lambda外切酶(lambda-exo)与感染高等真核生物的各种病毒编码的碱性外切核酸酶(AE)家族之间的遥远相似性。预测的结构相容和在功能上重要的残基在AE和ENase之间的保守性强烈地表明这些蛋白质之间存在着遥远的进化关系。根据广泛的序列数据库挖掘、序列/结构线索和分子模拟的结果，带有lambda-exo和其他一些假定的噬菌体编码的外切核酸酶的AE蛋白可能形成了一个不同的PD-(D/E)XK酶亚家族。用序列比对和距离矩阵方法推测该亚家族的系统发育历史。
The PD-(D/E)XK superfamily of deoxyribonucleases (ENases) comprises restriction endonucleases, exonucleases and nicking enzymes, which share a common fold and the architecture of the active site. Their extreme divergence generally hampers identification of novel members based solely on sequence comparisons. Here we report a remote similarity between the phage lambda exonuclease (lambda -exo), branching out early in the evolutionary history of ENases (3), with the family of alkaline exonucleases (AE) encoded by various viruses infecting higher Eukaryota. The predicted structural compatibility and the conservation of the functionally important residues between AE and ENases strongly suggest a distant evolutionary relationship between these proteins. According to the results of extensive sequence database mining, sequence/structure threading and molecular modeling it is plausible that the AE proteins with lambda -exo and some other putative phage-encoded exonucleases form a distinct subfamily of PD-(D/E)XK ENases. The phylogenetic history of this subfamily is inferred using sequence alignment and distance matrix methods.