4OBY | pdb_00004oby

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

• PDB DOI: https://doi.org/10.2210/pdb4OBY/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-08 Released: 2014-02-12 
• Deposition Author(s): Bi, K., Zheng, Y., Dong, J., Gao, F., Wang, J., Wang, Y., Gong, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Models: experimental

Literature

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

• PubMed: 24474195 
• DOI: https://doi.org/10.1007/s13238-013-0012-1
• Primary Citation Related Structures: 
  4OBY


• 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.02 kDa 
• Atom Count: 4,289 
• Modeled Residue Count: 564 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine--tRNA ligase	A	578	Escherichia coli K-12	Mutation(s): 0  Gene Names: argS, b1876, JW1865 EC: 6.1.1.19
UniProt
Find proteins for P11875 (Escherichia coli (strain K12)) Explore P11875  Go to UniProtKB:  P11875

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	B [auth A]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.599	α = 90
b = 94.136	β = 110.53
c = 62.717	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Bi, K., Zheng, Y., Dong, J., Gao, F., Wang, J., Wang, Y., Gong, W.

Revision History  

• 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