Receptor Site for the 5‘-Phosphate of Elongator tRNAs Governs Substrate Selection by Peptidyl-tRNA Hydrolase

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Abstract
Eubacterial peptidyl-tRNA hydrolase (PTH) recycles all N-blocked aminoacyl-tRNA molecules but initiator formyl-methionyl-tRNAfMet, the acceptor helix of which is characterized by a 1−72 mismatch. Positive selection by PTH of noninitiator tRNA molecules with a full 1−72 base pair is abolished, however, upon the removal of the 5‘-phosphate. The tRNA 5‘-phosphate plays therefore the role of a relay between the enzyme and the status of the 1−72 base pair. In this study, the receptor site for the 5‘-phosphate of elongator peptidyl-tRNAs and the position at the surface of PTH of the 3‘-end of complexed peptidyl-tRNA are identified by site-directed mutagenesis experiments. The former site comprehends two cationic side chains (K105 and R133) which are likely to clamp the phosphate. The second corresponds to a four asparagine cluster (N10, N21, N68, and N114). By using these two positional constraints, the acceptor arm of elongation factor Tu-bound Phe-tRNAPhe could be docked to PTH. Contacts involve the acceptor and TΨC stems. By comparing the obtained 3D model to that of EF−Tu:Phe-tRNAPhe crystalline complex in which the 5‘-phosphate of the ligand also lies between a K and an R side chain, we propose that, in both systems, the capacity of the 5‘-phosphate of a tRNA to reach or not a receptor site is the main identity element governing generic selection of elongator tRNAs. On the other hand, while the 1−72 mismatch acts as an antideterminant for PTH or EF−Tu recognition, it behaves as a positive determinant for the formylation of initiator Met-tRNAfMet.