FIGURE 9.

Proposed enzymatic mechanisms for protein-only (A) and RNA-based (B) RNase P enzymes. Both protein and RNA-based RNase P enzymes use at least two metal ions for phosphodiester bond hydrolysis. The metal ions in PRORP1 are positioned through conserved aspartate residues, whereas the RNA-based RNase P coordinates metal ions mainly using non-bridging phosphate oxygens. Metal I (M1) is proposed to coordinate the nucleophilic water molecule and aid in transition state stabilization by interaction with a non-bridging phosphate oxygen. Metal II (M2) is also proposed to stabilize the transition state and potentially coordinates the 3′-oxyanion leaving group to facilitate bond cleavage.