Decoding site

HYG-B on the ribosomal 30S subunit (on the 16S rRNA molecule) has been identified, characterized, and shown to be involved in the ribosomal decoding site, but has been shown to be distinct from that for other 2DOS-AGAs. 

The structure of the A-site RNA oligonucleotide reveals the nature of the decoding site in solution (Figure 5.3). Globally, the upper and lower stems of... 

Additional rings on paromomycin and gentamicin Cla point to a molecular explanation of why 4, 6 -disubstituted aminoglycosides are more specific for the A-site binding pocket and enhance the affinity of aminoglycosides for the decoding site. 

Kondo, J. Fran9ois, B. Urzhumtsev, A. Westhof, E. Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin. Angew. Chem. Int. Ed. Engl. 2006, 45, 3310-3314. 

Figure 5.2. Design of a model oligonucleotide for the decoding site. See text for full caption.

Accurate selection of translation termination factors to ribosomes containing a stop codon in the A-site is less well understood. A picture is only beginning to emerge as the bacterial 708 ribosome and class I release factor RF2 atomic models have recently been fitted into cryo-EM stmctures. Via multiple interactions RF2 connects the ribosomal decoding site with the PTC and functionally mimics a tRNA molecule in the A-site. In the complex RF2 is close to helices 18, 44, and 31 of the 168 rRNA, small subunit ribosomal protein 812, helices 69, 71, 89, and 92 of the 238 rRNA, the L7/L12 stalk, and protein LI 1 of the large subunit (Arkov et al. 2000 Klaholz et al. 2003 Rawat et al. 2003). The L7/L12 stalk inter-... 

The anticodon of the tRNA is base-paired with mRNA in the "decoding site" on the 30S subunit. The 3-CCA end with attached aminoacyl group lies in the peptidyltransferase site in the 50S subunit. (F) and (G) are courtesy of Cate et al.18... 

Figure 29-2 (A) Secondary structure model for the 1542-residue E. coli 16S rRNA based on comparative sequence analysis.733 Dots indicate G U or A G pairs dashes indicate G C or A U pairs. Strongly implied tertiary interactions are shown by solid green lines. Helix numbering according to Brimacombe. Courtesy of Robin Gutell. (B) Simplified schematic drawing of type often used. (C) Positions of the A, P, and E sites on the 30S ribosomal subunit from Carter et al7° (D) Stereoscopic view of the three-dimensional fold of the 16S RNA from Thermus thermophilus as revealed by X-ray structural analysis at 0.3 nm resolution. Features labeled are the head (H), beak (Be), neck (N), platform (P), shoulder (Sh), spur (Sp), and body (Bo). (E-H) Selected parts of the 16S RNA. In (E) and (F) the helices are numbered as in (A). (F) and (H) are stereoscopic views. The decoding site...

Shandrick S, Zhao Q, Han Q, Ayida BK, Takahashi M, Winters GC, Simonsen KB, Vourloumis D, Hermann T. Monitoring molecular recognition of the ribosomal decoding site. Angew. Chem. Int. Ed. Engl. 2004 43 3177-3182. 

Intensive efforts to understand the molecular basis of aminoglycoside recognition by the decoding site, accomplished both by NMR evaluation of solution structures and crystallographic evaluation of solid state structures, have now defined the differences between recognition by the prokaryotic and eukaryotic ribo-In prokaryotic A-site recognition, the aminodeoxysaccharide I inserts into the A-site helix and... 

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