Selection of circularly permuted ribozymes from Bacillus subtilis RNAse P by substrate binding
Pan, T.; Zhong, K.
Biochemistry 33(47): 14207-14212
1994
ISSN/ISBN: 0006-2960 PMID: 7524672 DOI: 10.1021/bi00251a032
Accession: 009390587
The effect of a single break in the phosphodiester backbone of Bacillus subtilis RNAse P RNA (P RNA) was examined using circular permutation analysis (CPA). This method reveals that many of the phosphodiester bonds in this catalytic RNA can be broken with little or no effect on substrate binding. Phosphate positions that show strong effects are located mostly in regions conserved among all RNAse P RNAs, or they are in regions known to interact directly with the pre-tRNA substrate. Two circularly permuted isomers of P RNA were constructed and analyzed in detail. The K-M for both circularly permuted isomers is nearly identical to that of the wild-type P RNA. Since the K-M of the P RNA is essentially the same as the binding constant to the substrate, this finding confirms the CPA results. The implications of backbone breakage are discussed with respect to folding and catalysis of the RNAse P RNA.