The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure

Abstract

Bulged-G motifs are ubiquitous internal RNA loops that provide specific recognition sites for proteins and RNAs. To establish the common and distinctive features of the motif we determined the structures of three variants and compared them with related structures. The variants are 27-nt mimics of the sarcin/ricin loop (SRL) from Escherichia coli 23S ribosomal RNA that is an essential part of the binding site for elongation factors (EFs). The wild-type SRL has now been determined at 1.04 A resolution, supplementing data obtained before at 1.11 A and allowing the first calculation of coordinate error for an RNA motif. The other two structures, having a viable (C2658U*G2663A) or a lethal mutation (C2658G*G2663C), were determined at 1.75 and 2.25 A resolution, respectively. Comparisons reveal that bulged-G motifs have a common hydration and geometry, with flexible junctions at flanking structural elements. Six conserved nucleotides preserve the fold of the motif; the remaining seven to nine vary in sequence and alter contacts in both grooves. Differences between accessible functional groups of the lethal mutation and those of the viable mutation and wild-type SRL may account for the impaired elongation factor binding to ribosomes with the C2658G*G2663C mutation and may underlie the lethal phenotype.

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

“…For example, the classic S-motif (Leontis and Westhof 1998;Correll et al 2003) shows a well-conserved pattern of suites by this analysis, as illustrated in Figure 5A. The strong S-shape of strand 1 is the most distinctive feature of S-motifs, formed by suites 1a, 5z, 4s, #a, and 1a, while suites 1a, 1e, and 1a form the inward-dented backbone and switch between base stacks characteristic of strand 2.…”

“…The GNRA tetraloop is perhaps the most classic example of an RNA structural motif, identified by comparative sequence analysis (Woese et al 1990), characterized structurally by NMR (Heus and Pardi 1991), later defined in high-resolution detail (Correll et al 2003), and recently reanalyzed (Hsiao et al 2006). Figure 6A labels the modular backbone annotation on three superimposed examples of GNRA tetraloops, and Figure 6B compares the GNRA modular string N1aG1gN1aR1aA1cN1a with translated equivalents in the earlier nucleotide, dinucleotide, and suite nomenclatures.…”

“…3B) and other global conformational attributes. 1c suites occur as a rather common but subtle difference within Aform, for instance, just past the end of GNRA tetraloops as at G2663 in the 1.04 Å resolution sarcin-ricin loop of ur0035/1Q9A (Correll et al 2003), or to accommodate a synG-antiA noncanonical base pair as at G6 and G22 of the ar0006/420D helix (Pan et al 1999). (Note: Coordinate files are designated here by their six-character NDB code followed by their four-character Protein Data Bank code.)…”

Role of the basic character of α-sarcin’s NH2-terminal β-hairpin in ribosome recognition and phospholipid interaction

“…Furthermore, structural characterization of different SRL-like oligoribonucleotides has revealed how these isolated structures adopt the same conformation as well [43][44][45], being indeed susceptible of specific recognition and cleavage by ribotoxins [42,46]. The toxin and SRL structural determinants involved in their mutual recognition have been identified and characterized [13][14][15]47]. However, this cleavage reaction against an isolated SRL-like RNA takes place at rates about 1000-fold slower than when using intact ribosomes [37,46] indicating that additional recognition elements are needed for the optimal ribotoxins' inactivation action against ribosomes.…”

Computational Methods for RNA Structure Validation and Improvement

“…Base pairs can deviate a fair amount from coplanarity but should maintain good H-bonding. There is simply not enough room for a purine-purine pair within an A-form helix, but occasionally a pyrimidine-pyrimidine singly H-bonded pair can be tolerated, such as the C-U that ends the helix below the S-motif in the rat sarcin-ricin loop (Correll et al, 1998) compared to the G-C pair in that position for E. coli (Correll, Beneken, Plantinga, Lubbers, & Chan, 2003). Comparing across phylogenetically related sequences, base pairing is very strongly conserved both in helices and in other structural motifs, as judged by "isosteric" replacements (Leontis & Westhof, 2001;Stombaugh, Zirbel, Westhof, & Leontis, 2009), but there are occasional surprises such as the hole in E. coli Phe tRNA next to the nonpaired position 26 base (Byrne, Konevega, Rodnina, & Antson, 2010;Dunkle et al, 2011).…”