Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.
RNA. 2010 Jan;16(1):1-9. doi: 10.1261/rna.1791310. Epub 2009 Nov 30.
Group II introns are self-splicing, mobile genetic elements that have fundamentally influenced the organization of terrestrial genomes. These large ribozymes remain important for gene expression in almost all forms of bacteria and eukaryotes and they are believed to share a common ancestry with the eukaryotic spliceosome that is required for processing all nuclear pre-mRNAs. The three-dimensional structure of a group IIC intron was recently determined by X-ray crystallography, making it possible to visualize the active site and the elaborate network of tertiary interactions that stabilize the molecule. Here we describe the molecular features of the active site in detail and evaluate their correspondence with prior biochemical, genetic, and phylogenetic analyses on group II introns. In addition, we evaluate the structural significance of RNA motifs within the intron core, such as the major-groove triple helix and the domain 5 bulge. Having combined what is known about the group II intron core, we then compare it with known structural features of U6 snRNA in the eukaryotic spliceosome. This analysis leads to a set of predictions for the molecular structure of the spliceosomal active site.
内含子 II 是自我剪接的可移动遗传元件，它们从根本上影响了陆地基因组的结构。这些大型核酶在几乎所有形式的细菌和真核生物中对于基因表达仍然很重要，并且它们被认为与真核剪接体具有共同的祖先，后者是加工所有核前体 mRNA 所必需的。通过 X 射线晶体学最近确定了一个内含子 IIIC 的三维结构，使得能够可视化活性位点和稳定分子的精细的三级相互作用网络。在这里，我们详细描述了活性位点的分子特征，并评估了它们与内含子 II 先前的生化、遗传和系统发育分析的对应关系。此外，我们评估了内含子核心内 RNA 模体的结构意义，例如主沟三螺旋和域 5 凸起。在结合了已知的内含子 II 核心信息后，我们将其与真核剪接体中 U6 snRNA 的已知结构特征进行了比较。这种分析导致了一组关于剪接体活性位点的分子结构的预测。
