2DXI

2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase

Sekine, S.Shichiri, M.Bernier, S.Chenevert, R.Lapointe, J.Yokoyama, S.

(2006) Structure 14: 1791-1799

  • DOI: 10.1016/j.str.2006.10.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glutamyl-tRNA synthetase (GluRS) is one of the aminoacyl-tRNA synthetases that require the cognate tRNA for specific amino acid recognition and activation. We analyzed the role of tRNA in amino acid recognition by crystallography. In the GluRS*tRNA(G ...

    Glutamyl-tRNA synthetase (GluRS) is one of the aminoacyl-tRNA synthetases that require the cognate tRNA for specific amino acid recognition and activation. We analyzed the role of tRNA in amino acid recognition by crystallography. In the GluRS*tRNA(Glu)*Glu structure, GluRS and tRNA(Glu) collaborate to form a highly complementary L-glutamate-binding site. This collaborative site is functional, as it is formed in the same manner in pretransition-state mimic, GluRS*tRNA(Glu)*ATP*Eol (a glutamate analog), and posttransition-state mimic, GluRS*tRNA(Glu)*ESA (a glutamyl-adenylate analog) structures. In contrast, in the GluRS*Glu structure, only GluRS forms the amino acid-binding site, which is defective and accounts for the binding of incorrect amino acids, such as D-glutamate and L-glutamine. Therefore, tRNA(Glu) is essential for formation of the completely functional binding site for L-glutamate. These structures, together with our previously described structures, reveal that tRNA plays a crucial role in accurate positioning of both L-glutamate and ATP, thus driving the amino acid activation.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, 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
tRNAC,D75N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
GAU
Query on GAU

Download SDF File 
Download CCD File 
A, B
(4S)-4-AMINO-5-HYDROXYPENTANOIC ACID
L-GLUTAMOL
C5 H11 N O3
JPYGFLFUDLRNKX-BYPYZUCNSA-N
 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: 2.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 110.615α = 90.00
b = 219.119β = 90.00
c = 135.816γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
HKL-2000data collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance