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Unformatted text preview: RNA tertiary interactions in the large ribosomal subunit: The A-minor motif 1. Poul Nissen * , 2. Joseph A. Ippolito * , 3. Nenad Ban * , 4. Peter B. Moore * , and 5. Thomas A. Steitz * + Author Affiliat ions 1. Departments of * Molecular Biophysics and Biochemistry, and Chemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114 1. Contributed by Peter B. Moore Next Section Abstract Analysis of the 2.4- resolut ion crystal st ructure of the large ribosomal subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2 OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3 terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A-minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large ribosomal subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. I t may prove to be the universally most important long-range interaction in large RNA structures. I t is well known that single-stranded RNAs fold back on themselves to form short, double-stranded helices that are stabilized primarily by WatsonCrick and GU wobble base pairs. In recent years, as increasing numbers of RNA structures have been determined, additional, rarer elements of RNA secondary structure ( 1 , 2 ) have been identified such as tetraloops ( 3 , 4 ), bulged-G motifs ( 5 7 ), and cross-stand purine stacks ( 5 , 7 , 8 ). Less is known about the ways RNAs with complex secondary structures fold to form RNA tertiary structure because few of the RNA structures known previously were large enough to have sufficient tertiary structure to analyze that problem. In contrast, the recently determined structures of the large ribosomal subunit from Haloarcula marismortui ( 9 , 10 ) and the small ribosomal subunit from Thermus thermophilus ( 11 , 12 ) contain a large number of long- range interactions between regions of RNA that are distant in the secondary structure. The 3,000 nt of the two RNAs of the large ribosomal subunit form a compact structure stabilized by tertiary interactions between secondary structure elements that include about 100 double helical stems. The st ructure of this large polyanion is stabilized, in part, by interactions with metal ions and proteins, which will be discussed elsewhere. Here we address the interactions occurring between and among RNA helices and single strands that stabilize RNA tert iary and quaternary st ructure.RNA helices and single strands that stabilize RNA tert iary and quaternary st ructure....
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