4Q2T

Crystal structure of Arginyl-tRNA synthetase complexed with L-arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The crystal structure of arginyl-tRNA synthetase from Homo sapiens

Kim, H.S.Cha, S.Y.Jo, C.H.Han, A.R.Hwang, K.Y.

(2014) FEBS Lett 588: 2328-2334

  • DOI: 10.1016/j.febslet.2014.05.027
  • Primary Citation of Related Structures:  
    4Q2T, 4Q2X, 4Q2Y

  • PubMed Abstract: 
  • Arginyl-tRNA synthetase (ArgRS) is a tRNA-binding protein that catalyzes the esterification of L-arginine to its cognate tRNA. L-Canavanine, a structural analog of L-arginine, has recently been studied as an anticancer agent. Here, we determined the crystal structures of the apo, L-arginine-complexed, and L-canavanine-complexed forms of the cytoplasmic free isoform of human ArgRS (hArgRS) ...

    Arginyl-tRNA synthetase (ArgRS) is a tRNA-binding protein that catalyzes the esterification of L-arginine to its cognate tRNA. L-Canavanine, a structural analog of L-arginine, has recently been studied as an anticancer agent. Here, we determined the crystal structures of the apo, L-arginine-complexed, and L-canavanine-complexed forms of the cytoplasmic free isoform of human ArgRS (hArgRS). Similar interactions were formed upon binding to L-canavanine or L-arginine, but the interaction between Tyr312 and the oxygen of the oxyguanidino group was a little bit different. Detailed conformational changes that occur upon substrate binding were explained. The hArgRS structure was also compared with previously reported homologue structures. The results presented here may provide a basis for the design of new anticancer drugs, such as L-canavanine analogs.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea. Electronic address: chahong@korea.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginine--tRNA ligase, cytoplasmicA, B607Homo sapiensMutation(s): 1 
Gene Names: RARSRARS1
EC: 6.1.1.19
Find proteins for P54136 (Homo sapiens)
Explore P54136 
Go to UniProtKB:  P54136
NIH Common Fund Data Resources
PHAROS:  P54136
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.485α = 90
b = 106.901β = 90
c = 175.248γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description