NMR SOLUTION STRUCTURE OF THE LEAD-DEPENDENT RIBOZYME - EVIDENCE FOR DYNAMICS IN RNA CATALYSIS

The NMR solution structure of a lead-dependent ribozyme, known as the leadzyme, is presented. This ribozyme is among the smallest of the kno wn catalytic RNAs, with an active site consisting of a six-nucleotide asymmetric internal loop. This loop has a roughly double-helical struc ture, including a protonated adenine-cytosine wobble base-pair, that p ositions the cytosine base 5' to the cleavage site in a double-helical conformation. The deviations from helical structure Consist of two bu lged guanosine residues, G7 and G9, where G7 is the residue 3' to the cleavage site. The scissile phosphate group of the leadzyme is not pos itioned for in-line nucleophilic attack. Therefore, a conformational r earrangement in the active site is required to reach the proposed tran sition state for this ribozyme. This is similar to previous observatio ns in X-ray studies of the hammerhead ribozyme, and emphasizes the nec essity for dynamic structural fluctuations in the catalytic mechanism of small ribozymes. A model for metal-binding in the leadzyme is propo sed in which a lead ion binds to a bulged guanine base that is critica l for leadzyme function. (C) 1998 Academic Press.