We have obtained precatalytic (enzyme-substrate complex) and postcatalytic (enzyme-product complex) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures.
Digital Object Identifier (DOI)
Chi, Young-In; Martick, Monika; Lares, Monica; Kim, Rosalind; Scott, William G.; and Kim, Sung-Hou, "Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis" (2008). Center for Structural Biology Faculty Publications. 1.