Revisiting the substrate recognition of bacterial ribonuclease P: in the view of the recognition of the base N73 in the substrate.

The RNA subunit of bacterial ribonuclease P (RNase P) is a ribozyme which can cleave a canonical cloverleaf tRNA precursor and a hairpin RNA with a CCA-3' tag sequence as its substrate. At high concentration of Mg ion, the substrate shape preference of the ribozyme becomes broader to accept a hairpin shape RNA. In hairpin RNA cleavage reactions, we found that the base interaction between the base U294 of E. coli ribozyme and the base N73 of the substrate RNA did not obey the response according to the Watson-Crick type interaction which is usually observed in the interaction between the base U294 of ribozyme and the base N73 of tRNA precursor.