5GRO

Crystal structure of the N-terminal anticodon-binding domain of non-discriminating aspartyl-tRNA synthetase from Helicobacter pylori

Summary for 5GRO

• Entry DOI: 10.2210/pdb5gro/pdb
• Descriptor: Aspartate--tRNA(Asp/Asn) ligase, GLYCEROL, butanoic acid, ... (5 entities in total)
• Functional Keywords: non-discriminating aspartyl-trna synthetase, anticodon-binding domain, helicobacter pylori, ligase
• Biological source: Helicobacter pylori 26695
• Cellular location: Cytoplasm : P56459
• Total number of polymer chains: 2
• Total formula weight: 26135.34

Authors

Songsiriritthigul, C.,Fuengfuloy, P.,Chen, C.-J.,Suebka, S.,Chuawong, P. (deposition date: 2016-08-12, release date: 2017-02-15, Last modification date: 2023-11-08)

Primary citation

Songsiriritthigul, C.,Suebka, S.,Chen, C.-J.,Fuengfuloy, P.,Chuawong, P.
Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori
Acta Crystallogr F Struct Biol Commun, 73:62-69, 2017

PubMed 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 and tRNA. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS) from the human-pathogenic bacterium Helicobacter pylori is reported at 2.0 Å resolution. The apo form of H. pylori ND-AspRS 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 and tRNA. 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 (GAGL and NPKL) 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 (GUC) and tRNA (GUU). The absence of the amide H atom allows both C and U bases to be accommodated in the tRNA-recognition site.

PubMed: 28177315
DOI: 10.1107/S2053230X16020586

Experimental method

X-RAY DIFFRACTION (2 Å)