Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex
Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex
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DOI：
10.1038/nature05080
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发表时间：
2006-09-07
期刊：
影响因子：
64.8
通讯作者：
Carrondo, Maria A.
中科院分区：
文献类型：
--
作者：
Frazao, Carlos;McVey, Colin E.;Carrondo, Maria A.
RNA降解是控制基因表达的决定性因素。RNA的成熟、周转和质量控制由许多不同种类的核糖核酸酶进行（1）。核糖核酸酶II（RNase II）是一种主要的核糖核酸外切酶，参与所有这些基本过程（1）;它可以独立发挥作用，也可以作为外泌体的一个组成部分，外泌体是一种重要的RNA降解多蛋白复合物（2）。RNase II样酶在所有三个生命王国中都有发现，但没有这个家族任何蛋白质的结构数据（1-5）。在这里，我们报告的X射线晶体结构的配体自由（在2.44埃分辨率）和RNA结合（在2.74埃分辨率）形式的大肠杆菌RNase II。与序列预测相反，结构显示RNase II被组织成四个结构域：两个冷休克结构域，一个RNB催化结构域，它具有前所未有的α β折叠，和一个S1结构域。该酶在两个不同的区域（“锚”和“催化”区域）与RNA建立接触，这两个区域协同作用以提供催化作用（6）。活性位点埋在RNB催化结构域内，在由四个保守序列基序形成的口袋中。该结构表明，催化口袋只能接触单链RNA，并解释了RNA与DNA切割的特异性。它还解释了RNA降解的动力学机制，为RNA移位和酶的加工能力提供了结构基础。我们提出了一个涉及关键保守残基的外切核酸降解RNA的反应机制。我们的三维模型证实了RNase II的所有现有生化数据，并阐明了RNA降解的一般基础。此外，它揭示了重要的结构特征，可以外推到这个家庭的其他成员。
RNA degradation is a determining factor in the control of gene expression. The maturation, turnover and quality control of RNA is performed by many different classes of ribonucleases(1). Ribonuclease II (RNase II) is a major exoribonuclease that intervenes in all of these fundamental processes(1); it can act independently or as a component of the exosome, an essential RNA-degrading multiprotein complex(2). RNase II-like enzymes are found in all three kingdoms of life, but there are no structural data for any of the proteins of this family(1-5). Here we report the X-ray crystallographic structures of both the ligand-free (at 2.44 angstrom resolution) and RNA-bound (at 2.74 angstrom resolution) forms of Escherichia coli RNase II. In contrast to sequence predictions, the structures show that RNase II is organized into four domains: two cold-shock domains, one RNB catalytic domain, which has an unprecedented alpha beta-fold, and one S1 domain. The enzyme establishes contacts with RNA in two distinct regions, the 'anchor' and the 'catalytic' regions, which act synergistically to provide catalysis(6). The active site is buried within the RNB catalytic domain, in a pocket formed by four conserved sequence motifs. The structure shows that the catalytic pocket is only accessible to single-stranded RNA, and explains the specificity for RNA versus DNA cleavage. It also explains the dynamic mechanism of RNA degradation by providing the structural basis for RNA translocation and enzyme processivity. We propose a reaction mechanism for exonucleolytic RNA degradation involving key conserved residues. Our three-dimensional model corroborates all existing biochemical data for RNase II, and elucidates the general basis for RNA degradation. Moreover, it reveals important structural features that can be extrapolated to other members of this family.