Book of Abstracts: Albany 2005
Crystal structure of a group I intron splicing intermediate
The group I intron is a self-splicing RNA that is able to remove itself from an RNA transcript while ligating the flanking exons. Its discovery led to a paradigm shift in biology by showing that not all cellular catalysts are proteins. We have determined the X-ray crystal structure of an intact intron in complex with both its exons. The structure includes the nucleophile, the scissile phosphate and the leaving group. This complex corresponds to the splicing intermediate prior to the exon ligation step. It reveals how the intron uses structurally unprecedented RNA motifs to select the 5'- and 3'-splice sites and how metal ions are positioned to act catalytically within the active site. The 5'-exon's 3'-OH is positioned for inline nucleophilic attack on the conformationally constrained scissile phosphate at the intron-3'-exon junction. Six phosphates from three disparate RNA strands converge to coordinate two metal ions that are asymmetrically positioned on opposing sides of the reactive phosphate. The metal activating the nucleophile is analogous to metal MA in all RNA and DNA polymerases. In these cases, the metal ion is coordinated to the carboxylate side chains of two or three amino acids in addition to the non-bridging oxygen of the scissile phosphate. Thus, the RNA intron is able to use its phosphate backbone to coordinate an active site metal ion in the same manner that a protein uses the side chains of aspartates and/or glutamates.
Department of Molecular Biophysics and Biochemistry