Crystal Structure of E.coli Arginyl-tRNA Synthetase and Ligand Binding Studies Revealed Key Residues in Arginine Recognition

Experimental Data Snapshot

  • Resolution: 2.57 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

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Crystal structure of E. coli arginyl-tRNA synthetase and ligand binding studies revealed key residues in arginine recognition.

Bi, K.Zheng, Y.Gao, F.Dong, J.Wang, J.Wang, Y.Gong, W.

(2014) Protein Cell 5: 151-159

  • DOI: https://doi.org/10.1007/s13238-013-0012-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The arginyl-tRNA synthetase (ArgRS) catalyzes the esterification reaction between L-arginine and its cognate tRNA(Arg). Previously reported structures of ArgRS shed considerable light on the tRNA recognition mechanism, while the aspect of amino acid binding in ArgRS remains largely unexplored. Here we report the first crystal structure of E. coli ArgRS (eArgRS) complexed with L-arginine, and a series of mutational studies using isothermal titration calorimetry (ITC). Combined with previously reported work on ArgRS, our results elucidated the structural and functional roles of a series of important residues in the active site, which furthered our understanding of this unique enzyme.

  • Organizational Affiliation

    Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginine--tRNA ligase578Escherichia coli K-12Mutation(s): 0 
Gene Names: argSb1876JW1865
Find proteins for P11875 (Escherichia coli (strain K12))
Explore P11875 
Go to UniProtKB:  P11875
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11875
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ARG

Download Ideal Coordinates CCD File 
C6 H15 N4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.57 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.599α = 90
b = 94.136β = 110.53
c = 62.717γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-04-02
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description