Protein synthesis in all organisms makes use of a molecular factory within the cell known as the ribosome. This molecular factory is made of ribonucleic acid and protein and works in a coordinated manner with various factors in a process known as translation. Understanding precisely how the ribosome functions provides useful avenues for drug discovery.

At the end of translation in bacteria, ribosome recycling factor (RRF) is used together with Elongation Factor G (EF-G) to recycle the 30S and 50S ribosomal subunits for the next round of translation. In this study we present the results of X-ray crystal structures of RRF with the Escherichia coli 70S ribosome. RRF binds to the large ribosomal subunit in the cleft that contains the peptidyl transferase center (PTC). Upon binding of either E. coli or T. thermophilus RRF to the E. coli ribosome, the tip of ribosomal RNA helix H69 in the large subunit moves away from the small subunit toward RRF by 8 Å, thereby disrupting a key contact between the small and large ribosomal subunits, termed bridge B2a. In the ribosome crystals, the ability of RRF to destabilize bridge B2a is influenced by crystal packing forces which are dependent upon the crystallization conditions used. Movement of helix H69 involves an ordered to disordered transition upon binding of RRF to the ribosome. The disruption of bridge B2a upon RRF binding to the ribosome seen in the present structures reveals one of the key roles that RRF plays in ribosome recycling, the dissociation of 70S ribosomes into subunits. The structures also reveal contacts between Domain II of RRF and protein S12 in the 30S subunit that may also play a role in ribosome recycling.

This study also presents X-ray crystal structures that demonstrate how the two antibiotics gentamicin and paromomycin physically inhibit the molecular mechanism by which RRF functions. Gentamicin and paromomycin bind to H69 and completely restore the contacts between ribosomal subunits that are disrupted by RRF. These results provide a structural explanation for how these antibiotics inhibit ribosome recycling and provide a useful avenue for new drug discovery.