Another burst of smoke: atomic resolution structures of RF3 bound to the ribosome

Abstract

Two recent reports provide atomic resolution information detailing the interaction of the class II release factor, RF3, with the bacterial ribosome. Differences in the composition of the two crystal forms allow us to learn a considerable amount about how translational GTPases engage the ribosome to facilitate and define conformational rearrangements involved in protein synthesis.

FIGURE 1.

Model of RF3 function on the ribosome, with boxed step indicating the structure defined in Zhou et al. (2011) and Jin et al. (2011). Steps are outlined as follows: (1) binding of class I release factor (RF1/2) to stop codon programmed ribosomes and catalysis of peptide release; (2) RF3 binding to the ribosome—it is unclear at this stage whether RF3 binds in its GTP- or GDP-bound state; additionally, the ribosome may be in a nonratcheted or ratcheted state (rotation lightly indicated); (3) RF1/2 dissociating from the ribosome; (4) RF3:GDPNP:ribosome complex characterized in Zhou et al. (2011) and Jin et al. (2011); ratcheted state of ribosome is indicated; (5) departure of RF3:GDP from the ribosome following GTP hydrolysis.

FIGURE 2.

(A) Crystal structure of RF3-GDPNP (green) on the ribosome (30S subunit in pale yellow and 50S subunit in pale blue). EFG (blue) aligned by G domain to the RF3 position in Zhou et al. (2011) allows domain IV of EFG to avoid steric clashes with the A site tRNA (orange). (B) EFG as seen in crystal structures with GDP and fusidic acid (red) (Gao et al. 2009) shows many steric clashes with A site tRNA as opposed to the EFG as aligned with RF3 G domain (again in blue).