Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase fromHelicobacter 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 tRNAAspand tRNAAsn. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS1–104) from the human-pathogenic bacteriumHelicobacter pyloriis reported at 2.0 Å resolution. The apo form ofH. pyloriND-AspRS1–104shares high structural similarity with the N-terminal anticodon-binding domains of the discriminating aspartyl-tRNA synthetase (D-AspRS) fromEscherichia coliand ND-AspRS fromPseudomonas aeruginosa, allowing recognition elements to be proposed for tRNAAspand tRNAAsn. It is proposed that a long loop (Arg77–Lys90) in thisH. pyloridomain influences its relaxed tRNA specificity, such that it is classified as nondiscriminating. A structural comparison between D-AspRS fromE. coliand ND-AspRS fromP. aeruginosasuggests that turns E and F (78GAGL81and83NPKL86) inH. pyloriND-AspRS play a crucial role in anticodon recognition. Accordingly, the conserved Pro84 in turn F facilitates the recognition of the anticodons of tRNAAsp(34GUC36) and tRNAAsn(34GUU36). The absence of the amide H atom allows both C and U bases to be accommodated in the tRNA-recognition site.