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Crucial role of an idiosyncratic insertion in the Rossman fold of class 1 aminoacyl-tRNA synthetases: the case of methionyl-tRNA synthetase.

A few aminoacyl-tRNA synthetases are characterized by their ability to tightly bind a zinc atom. In the case of Escherichia coli methionyl-tRNA synthetase, a peptide of 21 residues (138--163) having a stable 3-D structure in solution is responsible for zinc binding [Fourmy, D., Meinnel, T., Mechulam, Y., & Blanquet, S. (1993) J. Mol. Biol. 231, 1066--1077; Fourmy, D., Dardel, F., & Blanquet, S. (1993) J. Mol. Biol. 231, 1078--1089]. This peptide, which belongs to a region connecting the two halves of the nucleotide-binding domain of methionyl-tRNA synthetase, is likely to form a modular domain close to the active center of the enzyme. In this study, two residues of the zinc-binding module, Asp138 and Arg139, are shown to contribute to the stabilization of the transition state of the reaction leading to the activation of methionine. Moreover, another residue, Phe135, located at the surface of the zinc-binding domain, is found to possibly guide the tRNA acceptor stem toward the active site of the enzyme during catalysis. The available data indicate an important functional role for the zinc-binding module of methionyl-tRNA synthetase, as well as for other modules connecting conserved secondary structure elements in the aminoacyl-tRNA synthetase family. The relation between the occurrence of such variable peptide modules and the expression of both substrate specificity and catalytic efficiency is discussed.