Topology of Type II REases revisited; structural classes and the common conserved core.
Topology of Type II REases revisited; structural classes and the common conserved core.
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II型拓扑的重新审视；结构类别和共同保守的核心。
DOI：
10.1093/nar/gkm045
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发表时间：
2007
影响因子：
14.9
通讯作者：
Scheraga HA
中科院分区：
文献类型：
--
作者：
Niv MY;Ripoll DR;Vila JA;Liwo A;Vanamee ES;Aggarwal AK;Weinstein H;Scheraga HA
II型限制性内切酶是一种能切割DNA序列的脱氧核糖核酸酶，具有显著的特异性。II型酶在序列和拓扑上都有很大的差异，即二级结构元素的连通性。一个普遍的假设是，这些酶都有一个由五个β-链组成的结构核心，两侧有两个α-螺旋。我们介绍了一种系统的程序，以一种明确和可重复的方式列举二级结构元素，并用它来分析目前可用的II型折射体的X射线结构。基于这一分析，我们提出了核心的另一种定义，我们称之为αβα-核心。αβα-核心包括最常观察到的二级结构元件，不是三明治，因为它由五链β-折叠和在α-折叠的同一面上的两个β-螺旋组成。我们使用αβα核心连通性作为将类型II REAS分组为不同结构类的基础。在这些新的结构类中，连通性与二级结构元素之间的夹角和折叠体的切割模式相关。我们发现存在αβα-核心的一个亚结构，即一个共同的保守核心ccc，在这里定义为一个α-螺旋和四个β-链，对于所有已知结构的IIase来说都是共同的。
Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences with remarkable specificity. Type II REases are highly divergent in sequence as well as in topology, i.e. the connectivity of secondary structure elements. A widely held assumption is that a structural core of five β-strands flanked by two α-helices is common to these enzymes. We introduce a systematic procedure to enumerate secondary structure elements in an unambiguous and reproducible way, and use it to analyze the currently available X-ray structures of Type II REases. Based on this analysis, we propose an alternative definition of the core, which we term the αβα-core. The αβα-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand β-sheet and two α-helices on the same face of the β-sheet. We use the αβα-core connectivity as a basis for grouping the Type II REases into distinct structural classes. In these new structural classes, the connectivity correlates with the angles between the secondary structure elements and with the cleavage patterns of the REases. We show that there exists a substructure of the αβα-core, namely a common conserved core, ccc, defined here as one α-helix and four β-strands common to all Type II REase of known structure.
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影响因子：
14.9
作者：
Holm, L;Sander, C
通讯作者：
Sander, C
影响因子：
--
作者：
Chmiel, AA;Bujnicki, JM;Skowronek, KJ
通讯作者：
Skowronek, KJ
影响因子：
3.9
作者：
Bujnicki, JM
通讯作者：
Bujnicki, JM
影响因子：
3.5
作者：
CHENG, XD;BALENDIRAN, K;ANDERSON, JE
通讯作者：
ANDERSON, JE
影响因子：
14.9
作者：
Andreeva, A;Howorth, D;Murzin, AG
通讯作者：
Murzin, AG