Crystal Structures of the CP1 Domain from Thermus thermophilus Isoleucyl-tRNA Synthetase and Its Complex with L-Valine

Abstract

Isoleucyl-tRNA synthetase (IleRS) links tRNAIle with not only its cognate isoleucine but also the nearly cognate valine. The CP1 domain of IleRS deacylates, or edits, the mischarged Val-tRNAIle. We determined the crystal structures of the Thermus thermophilus IleRS CP1 domain alone, and in its complex with valine at 1.8- and 2.0-Å resolutions, respectively. In the complex structure, the Asp328 residue, which was shown to be critical for the editing reaction against Val-tRNA Ile by a previous mutational analysis, recognizes the valine NH 3+ group. The valine side chain binding pocket is only large enough to accommodate valine, and the placement of an isoleucine model in this location revealed that the additional methylene group of isoleucine would clash with HiS319. The H319A mutant of Escherichia coli IleRS reportedly deacylates the cognate Ile-tRNAIle in addition to Val-tRNAIle, indicating that the valine-binding mode found in this study represents that in the Val-tRNAIle editing reaction. Analyses of the Val-tRNAIle editing activities of T. thermophilus IleRS mutants revealed the importance of Thr228, Thr229, Thr230, and Asp328, which are coordinated with water molecules in the present structure. The structural model for the Val-adenosine moiety of Val-tRNAIle bound in the IleRS editing site revealed some interesting differences in the substrate binding and recognizing mechanisms between HeRS and T. thermophilus leucyl-tRNA synthetase. For example, the carbonyl oxygens of the amino acids are located opposite to each other, relative to the adenosine ribose ring, and are differently recognized.