Crystal structure of the N-terminal anticodonbinding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori

Abstract

The N terminal anticodon binding domain of the nondiscriminating aspartyl tRNA synthetase (ND AspRS) plays a crucial role in the recognition of both tRNA Asp and tRNA Asn. Here, the first X ray crystal structure of the N terminal domain of this enzyme (ND AspRS 1-104) from the human pathogenic bacterium Helicobacter pylori is reported at 2.0 Å resolution. The apo form of H. pylori ND AspRS 1-104 shares high structural similarity with the N terminal anticodon binding domains of the discriminating aspartyl tRNA synthetase (D AspRS) from Escherichia coli and ND AspRS from Pseudomonas aeruginosa, allowing recognition elements to be proposed for tRNA Asp and tRNA Asn. It is proposed that a long loop (Arg77-Lys90) in this H. pylori domain influences its relaxed tRNA specificity, such that it is classified as nondiscriminating. A structural comparison between D AspRS from E. coli and ND AspRS from P. aeruginosa suggests that turns E and F (78 GAGL 81 and 83 NPKL 86) in H. pylori ND AspRS play a crucial role in anticodon recognition. Accordingly, the conserved Pro84 in turn F facilitates the recognition of the anticodons of tRNA Asp (34 GUC 36) and tRNA Asn (34 GUU 36). The absence of the amide H atom allows both C and U bases to be accommodated in the tRNA recognition site.