The nucleolytic ribozymes catalyse site-specific phosphodiester cleavage and ligation transesterification reactions in RNA. How can RNA act as a catalyst when it has a small fraction of the catalytic resources of a protein ?
Current evidence points towards general acid-base catalysis by nucleolytic ribozymes in general. We have found that two nucleotides play a key role in the reaction mechanism of the Varkud satellite (VS) ribozyme, an adenine (A756) and a guanine (G638). We have determined the solution structure of the complete ribozyme using small-angle X-ray scattering, finding that both nucleotides are readily juxtaposed with the scissile phosphate. The pH dependence of the ribozyme cleavage reaction is consistent with general acid-base catalysis involving G638 and A756, and 5’ phosphorothiolate substitution experiments indicate that G638 is the general base and A756 the general acid for the cleavage reaction.
Despite having a very different overall structure, the active components of the hairpin ribozyme appear to be almost identical with those of the VS ribozyme. Guanine nucleotides also play a key catalytic role in the hammerhead and GlmS ribozymes. The HDV ribozyme also performs general acid-base catalysis, although a cytosine and metal ion are used. Most interestingly, GlmS appears to employ a bound glucosamine-6-phosphate molecule as general acid.
The intrinsic rate of catalysis by the VS ribozyme is comparable to that of the enzyme ribonuclease A. However, catalytic mechanisms based on nucleobase-mediated general acid-base catalysis are inherently limited by the unfavorable pKa values of the natural nucleobases, compared to that of histidine in proteins.