The adenosine wedge motif. (A) The secondary structures of the A-wedge-containing AGPMs found in the E. coli rRNA (Schuwirth et al. 2005). The template (left) is used for presentation of the secondary structures of the particular AGPMs (right). The names of the helices (Helix 1 and Helix 2) are provided. The 5′→3′ directions of individual strands are indicated by arrows. Strands P, Q, R, and S correspond to those in Figure 1 (left). In each helix, nucleotides and base pairs are shown as horizontal lines positioned at layers numbered from −3 to +1. For strands Q and S, the 5′→3′ direction of the polynucleotide chain corresponds to the move from a lower to a higher level, while for strands P and R, it is opposite. The base pairs at the 0-level are boxed. GU/WC stands for the allowed identities of the corresponding base pair (GU or WC). The juxtaposition of base pairs at the 0-level is shown in Figure 1 (right). At the −3-level, all structures contain only one external nucleotide −3P. The name of each motif starts with letter “S” or “L,” depending on the subunit, small or large, in which it is found, followed by the number in the rRNA polynucleotide chain of the internal nucleotide of the GU or equivalent base pair at the 0-level (Gagnon and Steinberg 2002). In each strand, only the nucleotide of the 0-level is numbered according to the standard E. coli rRNA numeration (Schuwirth et al. 2005). (B) Stereo view of the tertiary structure of AGPM L639 (PDB entry code 2aw4) (Schuwirth et al. 2005). Each nucleotide is colored as in (A, right). For nucleotide −3P, only the backbone and the ribose are shown. (C) A simplified representation of AGPM L639. Each nucleotide is shown as a base, while the lines between nucleotides stand for covalent connections. The riboses are provided only for nucleotides −3P and −3R. −3R (thick white) stands for the imaginary position of this nucleotide if strand R continued to the −3-level in the regular A-RNA conformation. The simultaneous presence of −3R and −3P would have made the space between their riboses too narrow to accommodate adenosines [−2Q;−2S].
