SUNY at Albany
June 19-23, 2001
Functional implications from the structure of the small ribosomal subunit in complex with edeine and the initiation factor 3 (IF3).
We determined and refined the 3.2 Angstrom structure of the 30S subunit (1). This model was used to determine the structures of three functionally relevant complexes (2). Two of these were obtained by soaking crystals of the 30S subunit of Thermus thermophilusin solutions containing edeine or the C-terminal domain of IF3 (IF3C). We localized edeine in the vicinity of the E-site, interacting with universally conserved nucleotides of 16S rRNA in Helices 24 (H24), H28, H44 and H45. Furthermore, the binding of edeine induces the formation of a new base pair, between C795 at the loop of H24 and G693 at the loop of H23. This base pair would impose constraints on the mobility of the platform, which is believed to move during translation. Our structure offers a good explanation as to why edeine blocks the path of the mRNA between the decoding region and the anti Shine-Dalgarno (anti-SD) region of the 16S rRNA in prokaryotes. Similarly, as to why edeine interferes with the AUG recognition process and thus hampers the formation of the 80S initiation complex in eukaryotes. Overall, the effect of edeine is to alter the path of the mRNA, thereby affecting initiation as well as tRNA binding to the P-site. We localized IF3C at the solvent side of the platform, close to the anti-SD region of the 16S rRNA. Based on this location we docked the N-terminal domain of IF3 onto the 30S structure and found that it should be placed in close proximity to the P-site.
The position of IF3C shows clearly that the anti-association activity of IF3C is not due to physical blockage of the inter-subunit interface, but rather the product of a change in the conformational dynamics of the subunit. It also explains the correlation between the binding of IF3 to the small ribosomal subunit and the requirement of prokaryotic mRNAs to interact with the anti-SD region of 16S rRNA for efficient translation.References and Footnotes
Max Planck Inst. for Molecular Genetics,
AG Ribosomen Ihnestr. 73 14195 Berlin Germany