The conserved A-site finger of the 23 S rRNA: Just one of the intersubunit bridges or a part of the allosteric communication pathway?

During the translocation of tRNAs and mRNA relative to the ribosome, the B1a, B1b and B1c bridges undergo the most extensive conformational changes among the bridges between the large and the small ribosomal subunits. The B1a bridge, also called the A-site finger (ASF), is formed by the 23 S rRNA helix 38, which is located right above the ribosomal A-site. Here, we deleted part of the ASF so that the B1a intersubunit bridge could not be formed (Delta B1a). The mutation led to a less efficient subunit association. A number of functional activities of the Delta B1a ribosomes, such as tRNA binding to the P and A-sites, translocation and EF-G-related GTPase reaction were preserved. A moderate decrease in EF-G-related GTPase stimulation by the P-site occupation by deacylated tRNA was observed. This suggests that the B1a bridge is not involved in the most basic steps of the elongation. cycle, but rather in the fine-tuning of the ribosomal activity. Chemical probing of ribosomes carrying the ASF truncation revealed structural differences in the 5 S rRNA and in the 23 S rRNA helices located between the peptidyltransferase center and the binding site of the elongation factors. Interestingly, reactivity changes were found in the P-loop, an important functional region of the 23 S rRNA. It is likely that the A-site finger, in addition to its role in subunit association, forms part of the system of allosteric signal exchanges between the small subunit decoding center and the functional centers on the large subunit. (c) 2005 Elsevier Ltd. All rights reserved.