Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function.
The Tetrahymena ribozyme derived from the self-splicing group I intron binds a 5'-splice site analog (S) and guanosine (G), catalyzing their conversion to a 5'-exon analog (P) and GA. Herein, we show that binding of guanosine is exceptionally slow, limiting the reaction at near neutral pH. Our results implicate a conformational rearrangement on guanosine binding, likely because the binding site is not prearranged in the absence of ligand. The fast accommodation of guanosine (10(2) to 10(3) x s(-1)) and prior structural data suggest local rather than global rearrangements, raising the possibility that folding of this and perhaps other large RNAs is not fully cooperative. Guanosine binding is accelerated by addition of residues that form helices, referred to as P9.0 and P10, immediately 5' and 3' to the guanosine. These rate enhancements provide evidence for binding intermediates that have the adjacent helices formed before accommodation of guanosine into its binding site. Because the ability to form the P9.0 and P10 helices distinguishes the guanosine at the correct 3'-splice site from other guanosine residues, the faster binding of the correct guanosine can enhance specificity of 3'-splice site selection. Thus, paradoxically, the absence of a preformed binding site and the resulting slow guanosine binding can contribute to splicing specificity by providing an opportunity for the adjacent helices to increase the rate of binding of the guanosine specifying the 3'-splice site.
Karbstein
Katrin
K
Department of Biochemistry, Stanford University, Stanford, CA 94305-5307, USA.
Herschlag
Daniel
D
D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D004305:Dose-Response Relationship, Drug; D005091:Exons; D006151:Guanosine / Q000737:chemistry / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D007438:Introns; D007700:Kinetics; D008024:Ligands; D008956:Models, Chemical; D011485:Protein Binding; D012313:RNA / Q000378:metabolism; D016337:RNA, Catalytic / Q000378:metabolism*; D013768:Tetrahymena / Q000378:metabolism*; D013816:Thermodynamics; D013997:Time Factors
D008024:Ligands; D016337:RNA, Catalytic; D006151:Guanosine; D012313:RNA