Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA

The protein component of ribonuclease P (RNase P) binds to the RNA subunit, forming a functional ribonucleoprotein complex in vivo and enhancing the a ffinity of the precursor tRNA (pre-tRNA) substrate. Photacrosslinking exper iments with pre-tRNA bound to RNase P reconstituted with the protein compon ent of Bacillus subtilis ribonuclease P (P protein) site specifically modif ied with a crosslinking reagent indicate that: (i) the central cleft of P p rotein directly interacts with the single-stranded 5' leader sequence of pr e-tRNA, and (ii) the orientation and register of the pre-tRNA leader sequen ce in the central cleft places the protein component in close proximity to the active site. This unique mode of interaction suggests that the catalyti c active site in RNase P occurs near the interface of RNA and protein. In c ontrast to other ribonucleoprotein complexes where the protein mainly stabi lizes the active tertiary fold of the RNA, a critical function of the prote in component of RNase P is to alter substrate specificity and enhance catal ytic efficiency.