Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily.
Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily.
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DOI：
10.1093/nar/gkf645
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发表时间：
2002-12-01
影响因子：
14.9
通讯作者：
Aravind L
中科院分区：
文献类型：
--
作者：
Mazumder R;Iyer LM;Vasudevan S;Aravind L
2′，3 ′环核苷酸磷酸二酯酶是真核生物中催化tRNA内含子剪接中至少两个不同步骤的酶。最近，来自酵母和植物拟南芥的这些酶的生物化学和结构已经被广泛研究。发现它们与细菌tRNA连接酶LigT和脊椎动物髓鞘相关的2′，3 ′磷酸二酯酶共享一个共同的活性位点，其特征在于两个保守的组氨酸。使用敏感的序列分析方法，我们表明，这些酶定义了一个大的超家族的预测磷酸酯酶与两个保守的组氨酸（因此2 H磷酸酯酶超家族）。我们确定了几个新的家庭的2 H磷酸酯酶，并提出了一个完整的进化分类这个超家族。我们还对这些蛋白质进行了结构-功能分析，并提出了不同家族在这个超家族中与RNA底物和蛋白质伴侣的不同相互作用的证据。特别是，我们发现，真核生物包含两个古老的家庭，这些蛋白质可能参与RNA加工，转录共激活和转录后基因沉默。另一个限于脊椎动物和昆虫的真核家族与乌巴和SH 3结构域结合，表明在信号转导中的作用。我们在某些逆转录病毒、轮状病毒和冠状病毒的多聚蛋白中检测到这些磷酸酯酶模块，它们可以在病毒RNA的加帽和加工中发挥作用。此外，我们提出了细菌中2 H磷酸酯酶的多个家族的证据，这些家族可能参与加工具有2′，3 ′环磷酸酯键的小分子。进化分析表明，2 H结构域出现之前，所有生命形式的最后一个共同祖先通过一个简单的结构单元，包含一个单一的催化组氨酸的复制。最初，这个结构域似乎参与了RNA加工，并且似乎在进化的后期被招募来执行各种其他功能。
2′,3′ Cyclic nucleotide phosphodiesterases are enzymes that catalyze at least two distinct steps in the splicing of tRNA introns in eukaryotes. Recently, the biochemistry and structure of these enzymes, from yeast and the plant Arabidopsis thaliana, have been extensively studied. They were found to share a common active site, characterized by two conserved histidines, with the bacterial tRNA-ligating enzyme LigT and the vertebrate myelin-associated 2′,3′ phosphodiesterases. Using sensitive sequence profile analysis methods, we show that these enzymes define a large superfamily of predicted phosphoesterases with two conserved histidines (hence 2H phosphoesterase superfamily). We identify several new families of 2H phosphoesterases and present a complete evolutionary classification of this superfamily. We also carry out a structure– function analysis of these proteins and present evidence for diverse interactions for different families, within this superfamily, with RNA substrates and protein partners. In particular, we show that eukaryotes contain two ancient families of these proteins that might be involved in RNA processing, transcriptional co-activation and post-transcriptional gene silencing. Another eukaryotic family restricted to vertebrates and insects is combined with UBA and SH3 domains suggesting a role in signal transduction. We detect these phosphoesterase modules in polyproteins of certain retroviruses, rotaviruses and coronaviruses, where they could function in capping and processing of viral RNAs. Furthermore, we present evidence for multiple families of 2H phosphoesterases in bacteria, which might be involved in the processing of small molecules with the 2′,3′ cyclic phosphoester linkages. The evolutionary analysis suggests that the 2H domain emerged through a duplication of a simple structural unit containing a single catalytic histidine prior to the last common ancestor of all life forms. Initially, this domain appears to have been involved in RNA processing and it appears to have been recruited to perform various other functions in later stages of evolution.
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影响因子：
56.9
作者：
CULVER, GM;MCCRAITH, SM;PHIZICKY, EM
通讯作者：
PHIZICKY, EM
影响因子：
5.6
作者：
Aravind, L;Koonin, EV
通讯作者：
Koonin, EV
影响因子：
11.4
作者：
Fraser, IDC;Tavalin, SJ;Scott, JD
通讯作者：
Scott, JD
影响因子：
13.8
作者：
Dandekar, T;Snel, B;Bork, P
通讯作者：
Bork, P
影响因子：
14.9
作者：
Aravind, L;Koonin, EV
通讯作者：
Koonin, EV