Substrate recognition by the leucyl/phenylalanyl-tRNA-protein transferase. Conservation within the enzyme family and localization to the trypsin-resistant domain.

The leucyl/phenylalanyl-tRNA-protein transferase (L/F-transferase) from Escherichia coli catalyzes a peptidyltransferase reaction that results in the N-terminal aminoacylation of acceptor proteins using Leu-, Phe-, and Met-tRNAs as amino acid donors. We demonstrated that L/F-transferase homologs are widely distributed throughout the eubacteria, supporting our proposal that the enzyme family is ancient and catalyzes early peptide bond synthesis. However, here we present data suggesting that the L/F-transferase is not a homolog of the peptidyltransferase enzymes involved in cell wall peptidoglycan biosynthesis in Gram-positive species, such as Staphylococcus aureus. A sequence comparison of the known L/F-transferase homologs began to identify the essential residues required to catalyze a peptidyltransferase reaction and revealed that <20% of the residues were invariant within the L/F-transferase family. Despite this sequence variation, substrate specificity was broadly conserved, and L/F-transferase homologs from Providencia stuartii, Vibrio cholerae, Neisseria gonorrhoeae, and the cyanobacterium Synechocystis sp. all complemented an E. coli aat mutant (lacking L/F-transferase activity) for the degradation of N-end rule substrates. In vitro comparison of the most divergent L/F-transferase homologs, from E. coli and the cyanobacterium Synechocystis sp., revealed near-complete conservation of both substrate specificity and secondary structure. Finally, we demonstrated that variants of the E. coli L/F-transferase, lacking either 33 or 78 N-terminal residues, retained measurable peptidyltransferase activity and wild type substrate specificity. Overall, our results identified an essential core of an L/F-transferase and revealed that a peptidyltransferase catalyst may be constructed from approximately 120 amino acids.