Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis

The leadzyme is a small RNA motif that catalyzes a site-specific, Pb 2+ -dependent cleavage reaction. As such, it is an example of a metal-dependent RNA enzyme. Here we describe the X-ray crystallographic structure of the leadzyme, which reveals two independent molecules per asymmetric unit. Both molecules feature an internal loop in which a bulged purine base stack twists away from the helical stem. This kinks the backbone, rendering the phosphodiester bond susceptible to cleavage. The independent molecules have different conformations: one leadzyme copy coordinates Mg 2+ , whereas the other binds only Ba 2+ or Pb 2+ . In the active site of the latter molecule, a single Ba 2+ ion coordinates the 2´-OH nucleophile, and appears to mimic the binding of catalytic lead. These observations allow a bond cleavage reaction to be modeled, which reveals the minimal structural features necessary for catalysis by this small ribozyme.