Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3

Abstract

The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3. The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site. Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline. The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA. The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its in¯uence on the conformational dynamics of the small ribosomal subunit.

Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA

“…24,25 These studies suggest that the 970 loop plays an important role in protein synthesis. This notion is supported by structural studies showing that the 970 loop forms part of the primary binding site for tetracycline 26,27 and by the isolation of a tetracycline-resistant strain of Helicobacter pylori that contains three mutations at positions 965, 966 and 967. 28 Here, we identify the sequence and structural motifs of the 970 loop nucleotides that are essential for ribosome function in bacteria and propose a model for the role of the 970 loop in protein synthesis.…”

Structural basis for the inhibition of the eukaryotic ribosome

“…In bacteria, edeine binds between the P-site and the E-site of the small subunit and impairs the binding of initiator tRNA to the P-site during initiation 32,33 . In the yeast ribosome, edeine binds to the same region but adopts a markedly different conformation than on the bacterial 30S subunit (Fig.…”

Ribosomal dynamics inferred from variations in experimental measurements

“…The mismatch regions of the 50S subunit are distributed around its periphery, primarily associated with its proteins. None of the matching RNA regions participate in ligand interactions in the 30S subunit, but many of these helices in the 50S (Pioletti et al 2001;Yusupov et al 2001;Klaholz et al 2003;Rawat et al 2003) and regions found to be flexible in comparative structural studies (see Matadeen et al 1999;Yusupov et al 2001;Ogle et al 2002;Klaholz et al 2003;Rawat et al 2003) mapped into crystal structures of the 30S subunit (PDB identification: 1GIX; Yusupov et al 2001). (D) Secondary structure diagram of the 23S RNA, 5S RNA, and associated proteins, colored in dark gold if data available for the region generally were in good agreement (<25% of mismatch); blue, >25% of mismatches; and gray, no data in our data set.…”