The crystal structures of T. thermophilus lysyl-tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA(Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue.

Abstract

The crystal structures of Thermus thermophilus lysyl‐tRNA synthetase, a class IIb aminoacyl‐tRNA synthetase, complexed with Escherchia coli tRNA(Lys)(mnm5 s2UUU) at 2.75 A resolution and with a T. thermophilus tRNA(Lys)(CUU) transcript at 2.9 A resolution are described. In both complexes only the tRNA anticodon stem‐loop is well ordered. The mode of binding of the anticodon stem‐loop to the N‐terminal beta‐barrel domain is similar to that previously found for the homologous class IIb aspartyl‐tRNA synthetase‐tRNA(Asp) complex except in the region of the wobble base 34 where either mnm5 s2U or C can be accommodated. The specific recognition of the other anticodon bases, U‐35 and U‐36, which are both major identity elements in the lysine system, is also described. Additional crystallographic data on a ternary complex with a lysyl‐adenylate analogue show that binding of the intermediate induces significant conformational changes in the vicinity of the active site of the enzyme.