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

The leadzyme is a small RNA motif that catalyzes a site-specific, Pb2+-depe ndent cleavage reaction. As such, it is an example of a metal-dependent RNA enzyme. Here we describe the X-ray crystallographic structure of the leadz yme, which reveals two independent molecules per asymmetric unit. Both mole cules feature an internal loop in which a bulged purine base stack twists a way from the helical stem. This kinks the backbone, rendering the phosphodi ester bond susceptible to cleavage. The independent molecules have differen t conformations: one leadzyme copy coordinates Mg2+, whereas the other bind s only Ba2+ or Pb2+. 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 cataly sis by this small ribozyme.