Yeast tRNA^Asp recognition by its cognate class II aminoacyl-tRNA synthetase

Abstract

AMINOACYL-RNA synthetases can be divided into two classes according to structural features inferred from sequence alignments^1–3. This classification correlates almost perfectly with the attachment of the amino acid to the 2'-OH (class I) or 3'-OH (class II) group of the terminal adenosine^4–6. Six subgroups of higher homology can be inferred from sequence analysis^7,8. The five aminoacyl-tRNA synthetases whose crystal structures are known (MetRS, TyrRS and GlnRS in class I, SerRS and AspRS in class II) ^9–13 belong to different subgroups. Two of them, GlnRS and AspRS, have been cocrystallized with their cognate tRNA^11,13. AspRS, like six other members of class II, is an a₂ dimer. Yeast tRNA^Asp exhibits five identity determinants: the three anticodon bases, the discriminator base G73 and the base pair G10-U25¹⁴. We report here that the refined crystal structure of AspRS com-plexed with tRNA^Asp at 2.9 A resolution reveals three regions of contact, each involving a domain of AspRS and at least one identity determinant of tRNA^Asp. The mode of binding of the acceptor stem of tRNA^Asp by AspRS can be generalized to class II aminoacyl-tRNA synthetases, whereas the deciphering of the anticodon, which involves a large conformational change of the loop and the formation of a bulge, is more specific to the aspartic system.