Abstract
Tripeptides with two consecutive prolines are the shortest and most frequent sequences causing ribosome stalling. The bacterial translation elongation factor P (EF-P) relieves the arrest, allowing protein biosynthesis to continue. A seven amino acids long loop between beta-strands β3/β4 is crucial for EF-P function and is modified at its tip by lysylation of lysine or rhamnosylation of arginine. Phylogenetic analyses unveiled an invariant proline in the -2 position of the modification site in EF Ps that utilize lysine modifications such as Escherichia coli. Bacteria with arginine modifications such as Pseudomonas putida have selected against it. Focusing on the EF-Ps from these two model organisms we demonstrate the importance of the β3/β4 loop composition for functionalization with chemically distinct modifications. Ultimately we show that amino acid changes in E. coli EF P are needed for switching the activation strategy from lysylation to rhamnosylation.
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