NMR structures of loop B RNAs from the stem-loop IV domain of the Enterovirus internal ribosome entry site:: A single C to U substitution drastically changes the shape and flexibility of RNA
NMR structures of loop B RNAs from the stem-loop IV domain of the Enterovirus internal ribosome entry site:: A single C to U substitution drastically changes the shape and flexibility of RNA
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DOI：
10.1021/bi0363228
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发表时间：
2004-05-18
期刊：
影响因子：
2.9
通讯作者：
James, TL
中科院分区：
文献类型：
--
作者：
Du, ZH;Ulyanov, NB;James, TL
正链RNA病毒的5'-非翻译区包含许多顺式作用RNA结构元件，这些元件对各种病毒过程（如复制、翻译和新病毒粒子的包装）都很重要。其中包括肠病毒（包括1型脊髓灰质炎病毒（PVI））内核糖体进入位点（IRES）内的茎环IV结构域的环B RNA。对PVI的研究表明，细胞多聚（rC）结合蛋白2 （PCBP2）的第一个KH （hnRNP - K同源）结构域对环B的特异性识别对于病毒mRNA的有效翻译至关重要。在这里，我们报告了两个具有代表性的肠病毒环B RNA序列变体的核磁共振溶液结构。这两种RNA变体在PCBP2 KH1结构域结合位点的六核苷酸不对称内环序列中只有一个位置（C和U）不同。令人惊讶的是，这两种rna在凸起区域的整体形状和局部动态上有很大的不同。含有5'-AUCCCU凸起序列的RNA呈整体L形。它的凸起核苷酸，尤其是最后四个，是高度灵活的，核磁共振不能很好地定义。具有5'-AUUCCU凸起序列的RNA整体呈U形，凸起序列仅具有有限的灵活性。对这两种RNA结构及其动态特性的详细分析，以及现有的序列数据和已知的KH结构域-RNA复合物结构，不仅提供了环状B RNA如何被PCBP2 KH1结构域识别的见解，而且还提出了结构灵活性与蛋白质识别的预先存在的结构特征之间可能存在的相关性。
The 5'-untranslated region of positive-strand RNA viruses harbors many cis-acting RNA structural elements that are important for various viral processes such as replication, translation, and packaging of new virions. Among these is loop B RNA of the stem-loop IV domain within the internal ribosomal entry site (IRES) of enteroviruses, including Poliovirus type 1 (PVI). Studies on PVI have shown that specific recognition of loop B by the first KH (hnRNP K homology) domain of cellular poly(rC)-binding protein 2 (PCBP2) is essential for efficient translation of the viral mRNA. Here we report the NMR solution structures of two representative sequence variants of enteroviral loop B RNA. The two RNA variants differ at only one position (C vs U) within a six-nucleotide asymmetric internal loop sequence that is the binding site for the PCBP2 KH1 domain. Surprisingly, the two RNAs are drastically different in the overall shape and local dynamics of the bulge region. The RNA with the 5'-AUCCCU bulge sequence adopts an overall L shape. Its bulge nucleotides, especially the last four, are highly flexible and not very well defined by NMR. The RNA with the 5'-AUUCCU bulge sequence adopts an overall U shape, and its bulge sequence exhibits only limited flexibility. A detailed analysis of the two RNA structures and their dynamic properties, as well as available sequence data and known KH domain-RNA complex structures, not only provides insights into how loop B RNA might be recognized by the PCBP2 KH1 domain but also suggests a possible correlation between structural flexibility and pre-existing structural features for protein recognition.