GU receptors of double helices mediate tRNA movement in the ribosome

Abstract

A new RNA structural motif consisting of two double helices closely packed via minor grooves is found in many places in the ribosome structure. The packing requires that a GU base pair in one helix be packed against a Watson-Crick pair in the other helix. Two such motifs mediate the interaction of the P- and E-tRNA with the large ribosomal subunit. Analysis of the particular positions of these two motifs in view of the available data on occupancy of tRNA-binding sites and structural changes in the ribosome during the elongation cycle suggests a distinct role for each motif in tRNA translocation.

Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch

“…Although the details of the interaction cannot be defined from these experiments, they suggest that there may be helical packing between the minor groove edges of aptamer 1 P1 and aptamer 2 P3b. Such helix-helix interactions along the minor groove have been seen in the structure of T. thermophilus 23S rRNA and characterized as ribo-base interactions and as the Along Groove Packing Motif (AGPM) (Gagnon and Steinberg 2002;Gagnon et al 2006;Laing et al 2009). Alternatively, an interaction that indirectly involves P3b could be facilitated through correct folding of the P3 stem of aptamer 2 such that nucleotides in the loop right below P3b make contact with P1.…”

The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate

“…The structural consequences of the GÁU base pairs on the U-helix are unknown, but the asymmetry of the wobble base pairs is expected to add structural variation and distinctive electrostatic surfaces to the major and minor grooves of the U-helix (Masquida and Westhof 2000;Varani and McClain 2000;Xu et al 2007). In other systems, GÁU base pairs sometimes play functional roles by forming cation binding sites (Fan et al 2005), anion binding sites (Masquida et al 1999), ligand binding sites (Chow and Barton 1992), RNA tertiary interactions sites (Gagnon and Steinberg 2002;Mokdad et al 2006), or protein recognition sites (Batey and Williamson 1996). GÁU base pairs generally lower the thermal stability of the double helix in a manner that depends on the sequence context and their positions relative to the helical ends (Sugimoto et al 1986;Mathews et al 1999).…”

The adenosine wedge: A new structural motif in ribosomal RNA

“…The structure of AGPM is characterized by an axial symmetry with the axis being about perpendicular to the planes of the base pairs at the 0-level. This symmetry has been discussed in detail previously (Gagnon and Steinberg 2002); its axis is shown in Figure 1 (left) by the dash-dotted line. When any of the two helices is rotated around this axis for 180°, it almost completely coincides with the other helix.…”

“…1, left). AGPM has been found in more than a dozen locations in ribosomal RNA, always having practically the same conformation well superposable with the conformations of other cases of the motif (Gagnon and Steinberg 2002;Mokdad et al 2006). The nomenclature of the helices, strands, levels, and individual nucleotides of AGPM is given in Figure 2A (left).…”

“…Here we present a new motif, the so-called adenosine wedge (A-wedge), which, among the available RNA structures, has been identified in three locations, all in the ribosomal RNA. The motif can be considered as an arrangement of three previously identified recurrent motifs, the along-groove packing motif (AGPM) (Gagnon and Steinberg 2002;Mokdad et al 2006), the A-minor motif (Doherty et al 2001;Nissen et al 2001), and the hook-turn motif (Szép et al 2003).…”