Identification of peptide sequences at the tRNA binding site of Escherichia coli methionyl-tRNA synthetase

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Abstract
Four different structural regions of Escherichia coli tRNAfMet have been covalently coupled to E. coli methionyl-tRNA synthetase (MetRS) by using a tRNA derivative carrying a lysine-reactive cross-linker. We have previously shown that this cross-linking occurs at the tRNA binding sites of the enzyme and involves reaction of only a small number of the potentially available lysine residues in the protein [Schulman, L.H., Valenzeula, D., and Pelka, H. (1981) Biochemistry 20, 6018-6023; Valenzuela, D., Leon, O., and Schulman, L.H. (1984) Biochem. Biophys. Res. Commun. 119, 677-684]. In this work, four of the cross-linked peptides have been identified. The tRNA-protein cross-linked complex was digested with trypsin, and the peptides attached to the tRNA were separated from the bulk of the tryptic peptides by anion-exchange chromatography. The tRNA-bound peptides were released by cleavage of the disulfide bond of the cross-linker and separated by reverse-phase high-pressue liquid chromatography, yielding five major peaks. Amino acid analysis indicated that four of these peaks contained single peptides. Sequence analysis showed that the peptides were cross-linked to tRNAfMet through lysine residues 402, 439, 465, and 640 in the primary sequence of MetRS. Binding of the tRNA therefore involves interactions with the carboxyl-terminal half of MetRS, while X-ray crystallographic data have shown the ATP binding site to be located in the N-terminal domain of the protein [Zelwer, C., Risler, J.L., and Brunie, S. (1982) J. Mol. Biol. 155, 63-81]. The methods developed for the present studies should be applicable to determination of peptide sequences at the tRNA binding sites of other proteins.