Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA

Abstract

We determined the solution structure of two 27-nt RNA hairpins and their complexes with cobalt(III)-hexammine (Co(NH₃)₆³⁺) by NMR spectroscopy. The RNA hairpins used in this study are the P4 region from Escherichia coli RNase P RNA and a C-to-U mutant that confers altered divalent metal-ion specificity (Ca²⁺ replaces Mg²⁺) for catalytic activity of this ribozyme. Co(NH₃)₆³⁺ is a useful spectroscopic probe for Mg(H₂O)₆²⁺-binding sites because both complexes have octahedral symmetry and have similar radii. The thermodynamics of binding to both RNA hairpins was studied using chemical shift changes upon titration with Mg²⁺, Ca²⁺, and Co(NH₃)₆³⁺. We found that the equilibrium binding constants for each of the metal ions was essentially unchanged when the P4 model RNA hairpin was mutated, although the NMR structures show that the RNA hairpins adopt different conformations. In the C-to-U mutant a C[bull ]G base pair is replaced by U[bull ]G, and the conserved bulged uridine in the P4 wild-type stem shifts in the 3′ direction by 1 nt. Intermolecular NOE cross-peaks between Co(NH₃)₆³⁺ and RNA protons were used to locate the site of Co(NH₃)₆³⁺ binding to both RNA hairpins. The metal ion binds in the major groove near a bulge loop, but is shifted 5′ by more than 1 bp in the mutant. The change of the metal-ion binding site provides a possible explanation for changes in catalytic activity of the mutant RNase P in the presence of Ca²⁺.