tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding

Abstract

The 2.2 A Ê crystal structure of a ternary complex formed by yeast arginyl-tRNA synthetase and its cognate tRNA Arg in the presence of the L-arginine substrate highlights new atomic features used for speci®c substrate recognition. This ®rst example of an active complex formed by a class Ia aminoacyl-tRNA synthetase and its natural cognate tRNA illustrates additional strategies used for speci®c tRNA selection. The enzyme speci®cally recognizes the D-loop and the anticodon of the tRNA, and the mutually induced ®t produces a conformation of the anticodon loop never seen before. Moreover, the anticodon binding triggers conformational changes in the catalytic center of the protein. The comparison with the 2.9 A Ê structure of a binary complex formed by yeast arginyl-tRNA synthetase and tRNA Arg reveals that L-arginine binding controls the correct positioning of the CCA end of the tRNA Arg . Important structural changes induced by substrate binding are observed in the enzyme. Several key residues of the active site play multiple roles in the catalytic pathway and thus highlight the structural dynamics of the aminoacylation reaction.

Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code

“…As with lysine, arginine is charged (+1), and arginine has significant hydrogen bonding potential. These distinguishing features of arginine are utilized in the ArgRS synthetic active site to exclude incorrect amino acids (PDB 1F7U) [36]. Proline is the only encoded imino acid, so proline is readily distinguished in the ProRS active site from other encoded amino acids.…”

Substrate‐induced conformational changes in Escherichia coli arginyl–tRNA synthetase observed by 19F NMR spectroscopy

“…Five Trp residues of E. coli ArgRS are located in interesting and crucial regions, of which conformations may be altered upon the substrate binding (yeast ArgRS structure; Fig. 1) [5,7]. The catalytic core for both amino acid activation and tRNA aminoacylation reactions in ArgRS, which forms the sca¡old for the Rossmann fold, is composed of two halves assembled from three peptides [5,7].…”

“…1) [5,7]. The catalytic core for both amino acid activation and tRNA aminoacylation reactions in ArgRS, which forms the sca¡old for the Rossmann fold, is composed of two halves assembled from three peptides [5,7]. The ¢rst half of the catalytic core contains two peptideŝ Lys143^Lys194 and Trp266^Gly293^while the second half includes residues Thr345^Thr410 in yeast ArgRS [5,7].…”

“…The catalytic core for both amino acid activation and tRNA aminoacylation reactions in ArgRS, which forms the sca¡old for the Rossmann fold, is composed of two halves assembled from three peptides [5,7]. The ¢rst half of the catalytic core contains two peptideŝ Lys143^Lys194 and Trp266^Gly293^while the second half includes residues Thr345^Thr410 in yeast ArgRS [5,7]. Trp162 (yeast Trp192) and Trp228 (yeast Trp266) residues are located at the edge of the ¢rst half of the catalytic core, while Trp349 (yeast Phe383) residue is in the second half.…”

“…Trp446 (yeast Trp475) is in the proximity of a tRNA anticodon stem binding element (a so-called 6 loop from Ser480 to Thr485 in yeast). Trp172 (yeast Gly202) residue is buried in the Ins-1 (yeast Gln195^Ile265) domain that inserts itself into the catalytic core [5,7]. Therefore, it is possible to probe the conformational changes involving these regions in solution with these probes.…”