Solution structure of a consensus stem-loop D RNA domain that plays important roles in regulating translation and replication in enteroviruses and rhinoviruses
Solution structure of a consensus stem-loop D RNA domain that plays important roles in regulating translation and replication in enteroviruses and rhinoviruses
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DOI：
10.1021/bi048973p
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发表时间：
2004-09-28
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;Yu, JH;James, TL
三叶草RNA的茎环D是肠道病毒和鼻病毒5 '-UTR内的高度保守结构域。茎环D RNA与病毒3C或3CD蛋白之间的相互作用构成了核糖核蛋白复合物的基本特征，其在调节病毒翻译和复制中起关键作用。在这里，我们报告的解决方案NMR结构的38个核苷酸的RNA的序列，包括整个茎环D结构域和对应的共识序列中发现的肠道病毒和鼻病毒。基于化学位移的微小差异，对应于脊髓灰质炎病毒1型和柯萨奇病毒B3的序列变体具有几乎相同的结构。除了常规的距离和扭转角限制之外，在结构测定中还使用了大量（136）H-1-C-13单键残余偶极耦合（RDC）值。纳入RDC限制对于在全球和地方实现明确定义的结构至关重要。共有茎-环D的结构是由具有摆动UG闭合碱基对的UACG四环加帽的伸长的A型螺旋茎。三个连续的嘧啶碱基对（两个UU和一个CU对）存在于螺旋茎的中间，创造了独特的局部结构特征，如显着加宽的大沟。二核苷酸凸起位于茎的基部附近。突起本身是灵活的，不像分子的其他部分那样明确，但侧翼碱基对是完整的。独特的结构元件的独特空间排列意味着它们可以协同作用以实现对病毒3C或3CD蛋白的最佳结合亲和力和特异性。
Stem-loop D from the cloverleaf RNA is a highly conserved domain within the 5'-UTR of enteroviruses and rhinoviruses. Interaction between the stem-loop D RNA and the viral 3C or 3CD proteins constitutes an essential feature of a ribonucleoprotein complex that plays a critical role in regulating viral translation and replication. Here we report the solution NMR structure of a 38-nucleotide RNA with a sequence that encompasses the entire stem-loop D domain and corresponds to the consensus sequence found in enteroviruses and rhinoviruses. Sequence variants corresponding to Poliovirus type 1 and Coxsackievirus B3 have virtually the same structure, based on small differences in chemical shifts. A substantial number (136) of H-1-C-13 one-bond residual dipolar coupling (RDC) values were used in the structure determination in addition to conventional distance and torsion angle restraints. Inclusion of the RDC restraints was essential for achieving well-defined structures, both globally and locally. The structure of the consensus stem-loop D is an elongated A-type helical stem capped by a UACG tetraloop with a wobble UG closing base pair. Three consecutive pyrimidine base pairs (two UU and one CU pair) are present in the middle of the helical stem, creating distinctive local structural features such as a dramatically widened major groove. A dinucleotide bulge is located near the base of the stem. The bulge itself is flexible and not as well defined as the other parts of the molecule, but the flanking base pairs are intact. The peculiar spatial arrangement of the distinctive structural elements implies that they may work synergistically to achieve optimal binding affinity and specificity toward the viral 3C or 3CD proteins.