Molecular modeling of the three-dimensional architecture of the RNA component of yeast RNase MRP

RNase mitochondrial RNA processing (MRP) is a ribonucleoprotein endoribonuc lease that is involved in RNA processing events in both the nucleus and the mitochondria. The MRP RNA is both structurally and evolutionarily related to RNase P, the ribonucleoprotein endoribonuclease that processes the 5'-en d of tRNAs. Previous analysis of the RNase MRP RNA by phylogenetic analysis and chemical modification has revealed strikingly conserved secondary stru ctural elements in all characterized RNase MRP RNAs. Utilizing successive c onstraint modeling and energy minimization I derived a three-dimensional mo del of the yeast RNase MRP RNA. The final model predicts several notable fe atures. First, the enzyme appears to contain two separate structural domain s, one that is highly conserved among all MRP and P RNAs and a second that is only conserved in MRP RNAs. Second, nearly all of the highly conserved n ucleotides cluster in the first domain around a long-range interaction (LRI -I). This LRI-I is characterized by a ubiquitous uridine base, which points into a cleft between these two structural domains generating a potential a ctive site for RNA cleavage. Third, helices III and IV (the yeast equivalen t of the To-binding site) model as a long extended helix. This region is be lieved to be the binding site of shared proteins between RNase P and RNase MRP and would provide a necessary platform for binding these seven proteins . Indeed, several residues conserved between the yeast MRP and P RNAs clust er in the central region of these helixes. Lastly, characterized mutations in the MRP RNA localize in the model based on their severity. Those mutatio ns with little or no effect on the activity of the enzyme localize to the p eriphery of the model, while the most severe mutations localize to the cent ral portion of the molecule where they would be predicted to cause large st ructural defects. (C) 1999 Academic Press.