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. 2014 Apr 10;5:170. doi: 10.3389/fmicb.2014.00170

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Copyright © 2014 Shimizu.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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A structural comparison of RF2-dependent (left panel) and ArfB-dependent (right panel) peptidyl-tRNA hydrolysis on the ribosome. In the normal translation process, RF2 binds to the ribosomal A site according to the interaction between the termination codon and the SPF motif (purple) in RF2. In the ArfA/RF2 ribosome rescue process, RF2 may bind to the A site similarly, albeit in a codon-independent and ArfA-dependent manner. ArfB binds to the A site according to the interaction between the C domain of ArfB (green) and the ribosome in a codon-independent manner. In both reactions, the hydrolysis of peptidyl-tRNA in the P site is catalyzed by a specific GGQ amino acid motif (light blue) in the conserved domain of RF2 (domain 3; red) or ArfB (N domain; red). The structural coordinates of the RF2-dependent and ArfB-dependent hydrolysis complexes were taken from PDB entries 3F1E (Korostelev et al., 2008) and 4DH9 (Gagnon et al., 2012), respectively.