A crystal structure of a portion of RNA provides researchers with new insight about a key process along the way to protein synthesis. Before protein synthesis can proceed, noncoding regions (introns) of mRNA must be removed and the coding regions (exons) joined together.
“This is the first structure that includes the complete intron and both exons locked in a conformation relevant for the splicing reaction,” says Scott A. Strobel, professor of molecular biophysics and biochemistry at Yale University. “All exon ligation reactions are chemically equivalent. This is the first time a splicing intermediate of any kind has been visualized.”
The group I self-splicing intron and exons analyzed structurally by Strobel and his colleagues are from the purple bacterium Azoarcus [Nature, published online June 2, http://dx.doi.org/10.1038/nature02642]. They captured the complex by replacing four RNA nucleotides with their DNA analogs, which reduces the splicing activity a millionfold.
“Obviously, splicing must be done precisely, and this structure reveals how the splice sites are selected,” Strobel says. The intron uses novel RNA motifs to select the splice sites. One of the splice sites (at the 3' end) is selected by interactions with the intron’s terminal nucleotide, whereas the other splice site is selected by an extensive network of tertiary interactions.
Strobel and his colleagues find structural evidence for two metal ions, Mg2+ and K+, associated with the active site. K+ seems to serve as a “place holder” for a second Mg2+ because K+ binds to the site in the structure with DNA substitutions but is replaced by Mg2+ in all-ribose structures. “This suggests that Mg2+ is the physiologically relevant catalytic metal ion and might explain why the 2'-deoxy substitution is so inhibitory,” Strobel says.