Selection of small molecules by the Tetrahymena catalytic center

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Abstract
The catalytic center in group I RNAs contains a selective binding site that accommodates both guanosine and L-arglnine. In order to understand the specificity of the RNA for small molecules, we analyzed 6 RNAs that vary in this region. Specificity for nucleotldes resides substantially in G264 rather than its paired nucleotide C311, and is expressed substantiaiiy in Km, with comparatlveiy ilttle variation in kcat kcat., is not notabiy perturbed even for RNAs with mispairs in the active-site helix. For 5 of 6 sequences, effects of RNA substitutions on arginine binding and GTP reactivity are proportionai, confirming that arginine contacts a subset of the groups occupied by G. As a result of particuiar mutations, reaction with GTP is decreased, and reaction with the naturai nucleotides UTP and ATP Is enhanced. Molecular modeling of these effects suggests that exceptionally flexibie placement of reactants may be an essential quailty of RNA catalyzed splicing. The specificity of the intron can be rationalized by a type of binding model not previously considered, in which the G/arginine site includes adjacent nucieotides (an ‘axial’ site), rather than a singie nucleotide, G264.