Crystal structure of the N-terminal anticodon-binding 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 (₇₈GAGL₈₁ and ₈₃NPKL₈₆) 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 (³⁴GUC³⁶) and tRNA^Asn (³⁴GUU³⁶). The absence of the amide H atom allows both C and U bases to be accommodated in the tRNA-recognition site.

Keywords: Helicobacter pylori; anticodon-binding domain; crystal structure; nondiscriminating aspartyl-tRNA synthetase.