Contributions of 2'-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA.
The ribozyme derived from the intervening sequence of Tetrahymena thermophila pre-rRNA catalyzes a site-specific endonuclease reaction with both RNA and DNA oligonucleotides: CCCUCUAAAAA + G<-->CCCUCU + GAAAAA. However, the RNA substrate (rS) binds approximately 10(4)-fold stronger than the DNA substrate (dS) and once bound reacts approximately 10(4)-fold faster. Here we have investigated the role of individual 2'-hydroxyl groups by comparing the binding and reactivity of "chimeric" oligonucleotide substrates, in which the 2'-substituents of the individual sugar residues have been varied. Chimeric substrates containing a single ribonucleotide at positions -6 to +3 (numbered from the cleavage site) were cleaved faster than dS by factors of 3.5, 3.5, 2.3, 65, 18, 1700, 7.8, 1.7, and 1.4 [(kcat/Km)chimeric S/(kcat/Km)dS]. The sum of the energetic contributions from the individual 2'-hydroxyl groups of 13.3 kcal/mol accounts for the 12.2 kcal/mol greater stabilization for RNA than for DNA in binding and cleavage (i.e., overall transition-state stabilization). This observation and the significant energetic effects from single ribose substitutions at opositions-3 to +1 strongly suggest that local interactions, rather than overall helical differences, largely account for the different binding and reactivity of the DNA and RNA substrates. Each 2'-hydroxyl group was evaluated for its effect on each of three reaction steps leading to the chemical transition state: two binding steps (duplex formation and docking into tertiary interactions) and the chemical cleavage step. The 2'-hydroxyl groups at positions -3 and -2 stabilize docking, and this stabilization is maintained in the chemical step. This "uniform binding" indicates that these interactions contribute to catalysis by positioning the oligonucleotide substrate for reaction. The 2'-hydroxyl at position +1 has a small effect on the binding step and an additional small but significant effect on the chemical step. Thus, the ribozyme, like protein enzymes, can take advantage of interactions away from the site of chemistry to provide stabilization specifically in the transition state. The 2'-hydroxyl at position -1 exerts its large effect nearly exclusively on the chemical step [Herschlag, D., Eckstein, F., & Cech, T.R. (1993) Biochemistry (following paper in this issue)]. The energetic effects of other modifications of the 2'-substituents provide a crude picture of the active site. The 2'-OCH3 substituent at position -3 inhibits the reaction approximately 10-fold relative to 2'-H, suggesting than an unfavorable interaction cannot be avoided by an isoenergetic structural rearrangement.(ABSTRACT TRUNCATED AT 400 WORDS)
Herschlag
D
D
Department of Biochemistry, Beckman Center, Stanford University, California 94305-5307.
Eckstein
F
F
Cech
T R
TR
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D002384:Catalysis; D004247:DNA / Q000378:metabolism; D006860:Hydrogen Bonding; D007700:Kinetics; D008745:Methylation; D008969:Molecular Sequence Data; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D012322:RNA Precursors / Q000378:metabolism*; D016337:RNA, Catalytic / Q000378:metabolism*; D012266:Ribose / Q000378:metabolism; D013379:Substrate Specificity; D016808:Tetrahymena thermophila / Q000235:genetics*; D013816:Thermodynamics
D012322:RNA Precursors; D016337:RNA, Catalytic; D012313:RNA; D012266:Ribose; D004247:DNA