2HRA

Crystal structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA aminoacylation and nuclear export cofactor Arc1p reveal a novel function for an old fold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA-aminoacylation and nuclear-export cofactor Arc1p reveal a novel function for an old fold.

Simader, H.Hothorn, M.Suck, D.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1510-1519

  • DOI: 10.1107/S0907444906039850
  • Primary Citation of Related Structures:  
    2HQT, 2HRA

  • PubMed Abstract: 
  • Eukaryotic aminoacyl-tRNA synthetases (aaRS) frequently contain additional appended domains that are absent from their prokaryotic counterparts which mediate complex formation between eukaryotic aaRS and cofactors of aminoacylation and translation. However, the structural basis of such interactions has remained elusive ...

    Eukaryotic aminoacyl-tRNA synthetases (aaRS) frequently contain additional appended domains that are absent from their prokaryotic counterparts which mediate complex formation between eukaryotic aaRS and cofactors of aminoacylation and translation. However, the structural basis of such interactions has remained elusive. The heteromerization domain of yeast glutamyl-tRNA synthetase (GluRS) has been cloned, expressed, purified and crystallized in space group C222(1), with unit-cell parameters a = 52, b = 107, c = 168 A. Phase information was obtained from multiple-wavelength anomalous dispersion with selenomethionine to 2.5 A resolution and the structure, comprising two monomers per asymmetric unit, was determined and refined to 1.9 A resolution. The structure of the interacting domain of its accessory protein Arc1p was determined and refined to 1.9 A resolution in a crystal form containing 20 monomers organized in five tetramers per asymmetric unit (space group C2, unit-cell parameters a = 222, b = 89, c = 127 A, beta = 99.4 degrees ). Both domains adopt a GST-like fold, demonstrating a novel role for this fold as a protein-protein interaction module.


    Related Citations: 
    • Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
      Simader, H., Hothorn, M., Koehler, C., Basquin, J., Simos, G., Suck, D.
      () To be published --: --

    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA synthetase, cytoplasmicA, B209Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GUS1
EC: 6.1.1.17
UniProt
Find proteins for P46655 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46655 
Go to UniProtKB:  P46655
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , C [auth A] , CA [auth B] , D [auth A] , DA [auth B] , E [auth A] , EA [auth B] , 
AA [auth B],  BA [auth B],  C [auth A],  CA [auth B],  D [auth A],  DA [auth B],  E [auth A],  EA [auth B],  F [auth A],  FA [auth B],  G [auth A],  GA [auth B],  H [auth A],  HA [auth B],  I [auth A],  IA [auth B],  J [auth A],  JA [auth B],  K [auth A],  KA [auth B],  L [auth A],  LA [auth B],  M [auth A],  MA [auth B],  N [auth A],  NA [auth B],  O [auth A],  OA [auth B],  P [auth A],  PA [auth B],  Q [auth A],  QA [auth B],  R [auth A],  RA [auth B],  S [auth A],  SA [auth B],  T [auth A],  TA [auth B],  U [auth A],  V [auth A],  W [auth B],  X [auth B],  Y [auth B],  Z [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.959α = 90
b = 107.113β = 90
c = 167.865γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDphasing
SOLVEphasing
RESOLVEphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description