RNA. 2013 Oct;19(10):1349-54. doi: 10.1261/rna.038828.113. Epub 2013 Aug 12.
The highly conserved peptidyl transferase center (PTC) of the ribosome contains an RNA pore that serves as the entrance to the exit tunnel. Analysis of available ribosome crystal structures has revealed the presence of multiple additional well-defined pores of comparable size in the ribosomal (rRNA) RNAs. These typically have dimensions of 1-2 nm, with a total area of ∼100 Å(2) or more, and most are associated with one or more ribosomal proteins. The PTC example and the other rRNA pores result from the packing of helices. However, in the non-PTC cases the nitrogenous bases do not protrude into the pore, thereby limiting the potential for hydrogen bonding within the pore. Instead, it is the RNA backbone that largely defines the pore likely resulting in a negatively charged environment. In many but not all cases, ribosomal proteins are associated with the pores to a greater or lesser extent. With the exception of the PTC case, the large subunit pores are not found in what are thought to be the evolutionarily oldest regions of the 23S rRNA. The unusual nature of the PTC pore may reflect a history of being created by hybridization between two or more RNAs early in evolution rather than simple folding of a single RNA. An initial survey of nonribosomal RNA crystal structures revealed additional pores, thereby showing that they are likely a general feature of RNA tertiary structure.
核糖体高度保守的肽基转移酶中心 (PTC) 包含一个 RNA 孔，作为出口隧道的入口。对现有核糖体晶体结构的分析揭示了核糖体 (rRNA) RNA 中存在多个大小相当的额外明确的孔。这些孔通常尺寸为 1-2nm，总面积约为 100Å2 或更大，大多数与一个或多个核糖体蛋白相关。PTC 示例和其他 rRNA 孔是由螺旋包装形成的。然而，在非 PTC 情况下，含氮碱基不会突入孔内，从而限制了孔内氢键的形成潜力。相反，RNA 骨架在很大程度上定义了孔，可能导致带负电荷的环境。在许多但不是所有情况下，核糖体蛋白或多或少地与孔相关联。除了 PTC 情况外，大亚基孔不存在于被认为是 23S rRNA 中进化最古老的区域。PTC 孔的异常性质可能反映了在进化早期由两个或多个 RNA 杂交而不是单个 RNA 折叠形成的历史。对非核糖体 RNA 晶体结构的初步调查揭示了其他孔，从而表明它们可能是 RNA 三级结构的普遍特征。
