Fuxing Zeng, Yanbo Chen, Jonathan Remis, Mrinal Shekhar, James C. Phillips,
Emad Tajkhorshid, and Hong Jin.
Structural basis of co-translational quality control by ArfA and
RF2 bound to ribosome.
Nature, 541:554-557, 2017.
(PMC: PMC5679781)
ZENG2017-ET
Quality control mechanisms intervene appropriately when defective translation
events occur, in order to preserve the integrity of protein synthesis. Rescue of
ribosomes translating on messenger RNAs that lack stop codons is one of the
co-translational quality control pathways. In many bacteria, ArfA recognizes
stalled ribosomes and recruits the release factor RF2, which catalyses the
termination of protein synthesis1, 2, 3. Although an induced-fit mechanism of
nonstop mRNA surveillance mediated by ArfA and RF2 has been reported4, the
molecular interaction between ArfA and RF2 in the ribosome that is responsible
for the mechanism is unknown. Here we report an electron cryo-microscopy
structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop
mRNA. The structure, which is consistent with our kinetic and biochemical data,
reveals the molecular interactions that enable ArfA to specifically recruit RF2,
not RF1, into the ribosome and to enable RF2 to release the truncated protein
product in this co-translational quality control pathway. The positively charged
C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome.
Furthermore, binding of ArfA and RF2 induces conformational changes in the
ribosomal decoding centre that are similar to those seen in other protein-
involved decoding processes. Specific interactions between residues in the N-
terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent
conformation for peptide release. Our findings provide a framework for
understanding recognition of the translational state of the ribosome by new
proteins, and expand our knowledge of the decoding potential of the ribosome.
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