5GRO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

Songsiriritthigul, C.Suebka, S.Chen, C.-J.Fuengfuloy, P.Chuawong, P.

(2017) Acta Crystallogr F Struct Biol Commun 73: 62-69

  • DOI: 10.1107/S2053230X16020586
  • Primary Citation of Related Structures:  
    5GRO

  • 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 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, and Special Research Unit for Advanced Magnetic Resonance, Kasetsart University, 50 Ngamwongwan Road, Chatuchak, Bangkok 10900, Thailand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate--tRNA(Asp/Asn) ligaseAB115Helicobacter pylori 26695Mutation(s): 0 
Gene Names: aspSHP_0617
EC: 6.1.1.23
Find proteins for P56459 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56459 
Go to UniProtKB:  P56459
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BUA
Query on BUA

Download CCD File 
B
BUTANOIC ACID
C4 H8 O2
FERIUCNNQQJTOY-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download CCD File 
B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.83α = 90
b = 61.83β = 90
c = 141.376γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Center of Excellence for Innovation in Chemistry (PERCH-CIC)Thailand--
Synchrotron Light Research Institute (SLRI)Thailand--

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references