RNase MRP and RNase P are both ribonucleoprotein
enzymes performing endonucleolytic cleavage of RNA. RNase
MRP cleaves at a specific site in the precursor-rRNA transcript
to initiate processing of the 5.8S rRNA. RNase P cleaves
precursor tRNAs to create the 5′ end of the mature
tRNAs. In spite of their different specificities, the two
RNases have significant structural similarities. For example,
the two enzymes in Saccharomyces cerevisiae share
eight protein subunits; only one protein is unique to each
enzyme. The RNA components of the two nucleases also show
striking secondary-structure similarity. To begin to characterize
the role of the RNA subunits in enzyme function and substrate
specificity, we swapped two hairpin structures (MRP3 and
P3) between RNase MRP RNA and RNase P RNA of S. cerevisiae.
The hairpins in the two enzymes could be exchanged without
loss of function or specificity. On the other hand, when
the MRP3 hairpin in RNase MRP of S. cerevisiae
was replaced with the corresponding hairpin from the RNA
of Schizosaccharomyces pombe or human RNase MRP,
no functional enzyme was assembled. We propose that the
MRP3 and P3 hairpins in S. cerevisiae perform
similar functions and have coevolved to maintain common
features that are different from those of MRP3 and P3 hairpins
in other species.