1N78

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding

Sekine, S.Nureki, O.Dubois, D.Y.Bernier, S.Chenevert, R.Lapointe, J.Vassylyev, D.G.Yokoyama, S.

(2003) EMBO J. 22: 676-688

  • DOI: 10.1093/emboj/cdg053
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism ...

    Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.


    Related Citations: 
    • Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase
      Sekine, S.,Nureki, O.,Shimada, A.,Vassylyev, D.G.,Yokoyama, S.
      (2001) Nat.Struct.Mol.Biol. 8: 203
    • Architectures of class-defining and specific domains of glutamyl-tRNA synthetase
      Nureki, O.,Vassylyev, D.G.,Katayanagi, K.,Shimizu, T.,Sekine, S.,Kigawa, T.,Miyazawa, T.,Yokoyama, S.,Morikawa, K.
      (1995) Science 267: 1958


    Organizational Affiliation

    Cellular Signaling Laboratory and Structurome Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamyl-tRNA synthetase
A, B
468Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: gltX
EC: 6.1.1.17
Find proteins for P27000 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P27000
Entity ID: 1
MoleculeChainsLengthOrganism
tRNA(Glu)C,D75N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOM
Query on GOM

Download SDF File 
Download CCD File 
A, B
GLUTAMOL-AMP
C15 H22 N6 O9 P
JDELUWYDJMPPMI-SBZSCLMQSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 110.492α = 90.00
b = 219.870β = 90.00
c = 135.119γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance