5gro | pdb_00005gro

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

spinqualitylabelsall models 5gro, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5gro is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: BUA, GOL, IMD Activity: Aspartate--tRNA(Asn) ligase, with EC number 6.1.1.23 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [SYDND_HELPY] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.7 times more efficient at aminoacylating tRNA(Asp) over tRNA(Asn). Reaction proceeds in two steps: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn). Publication Abstract from PubMed The N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) plays a crucial role in the recognition of both tRNAAsp and tRNAAsn. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS1-104) from the human-pathogenic bacterium Helicobacter pylori is reported at 2.0 A resolution. The apo form of H. pylori ND-AspRS1-104 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 tRNAAsp and tRNAAsn. 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 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. Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori.,Songsiriritthigul C, Suebka S, Chen CJ, Fuengfuloy P, Chuawong P Acta Crystallogr F Struct Biol Commun. 2017 Feb 1;73(Pt 2):62-69. doi:, 10.1107/S2053230X16020586. Epub 2017 Jan 19. PMID:28177315 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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