RNA tertiary interactions in the large ribosomal subunit: The A-minor motif

Abstract

Analysis of the 2.4-Å resolution crystal structure 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. It may prove to be the universally most important long-range interaction in large RNA structures. It is well known that single-stranded RNAs fold back on themselves to form short, double-stranded helices that are stabilized primarily by Watson-Crick 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 Ϸ3,000 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 structure 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 tertiary and quaternary structure. MethodsFor our study, each adenosine residue in the structure of the H. marismortui 23S rRNA (Protein DataBank entry 1FFK) was assessed for occurrences of A-minor interactions by using the graphics program O (13). A-minor interactions were selected based on the following predetermined geometric criteria. The C2 atom of the adenosine had to be within 3.7 Å of one of its neighboring atoms. The interacting atom had to lie within 45°of the adenine plane. Finally, the C2 face of the adenosine had t...

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“…6b) pairs. The selected viewpoints highlight the very different types of interactions of adenine with the minor-groove edges of the G·C pairs in the two pentaplets, i.e., distinct types of A-minor motifs 68 . Whereas A2010 approaches G2013 (Fig.…”

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

“…It was first identified by phylogeny in group I and II introns by Michel, Westhof, and colleagues and observed for the first time in the seminal crystal structure of the P4-P6 domain of the Tetrahymena group I intron, in which this motif reinforces the side-by-side packing architecture of RNA helices [84][85][86]. This motif and others are ubiquitous in the ribosome and other structured RNAs [87][88][89][90][91]. We wish to emphasize that information on motif partners and secondary structuredetermined from phylogeny -provides a powerful tool in modeling RNA structure.…”

Structural features of metabolite-sensing riboswitches

“…Another common RNA building unit, the GNRA tetraloop, is present within the glmS ribozyme and mediates direct contact between distantly located regions of the molecule (P1, P4) (Figure 1e and 2e) [31]. Finally, A-minor motifs [45], which result from the docking of adenosines into the minor groove of a distantly located base pair, are common within riboswitch structures and are integral components for tertiary structure stabilization. In addition to these motifs riboswitches can also contain unique structural elements.…”