3AFH

Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with a glutamyl-AMP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of nondiscriminating glutamyl-tRNA synthetase from Thermotoga maritima

Ito, T.Kiyasu, N.Matsunaga, R.Takahashi, S.Yokoyama, S.

(2010) Acta Crystallogr.,Sect.D 66: 813-820

  • DOI: 10.1107/S0907444910019086

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases produce aminoacyl-tRNAs from the substrate tRNA and its cognate amino acid with the aid of ATP. Two types of glutamyl-tRNA synthetase (GluRS) have been discovered: discriminating GluRS (D-GluRS) and nondiscriminating GluRS ...

    Aminoacyl-tRNA synthetases produce aminoacyl-tRNAs from the substrate tRNA and its cognate amino acid with the aid of ATP. Two types of glutamyl-tRNA synthetase (GluRS) have been discovered: discriminating GluRS (D-GluRS) and nondiscriminating GluRS (ND-GluRS). D-GluRS glutamylates tRNA(Glu) only, while ND-GluRS glutamylates both tRNA(Glu) and tRNA(Gln). ND-GluRS produces the intermediate Glu-tRNA(Gln), which is converted to Gln-tRNA(Gln) by Glu-tRNA(Gln) amidotransferase. Two GluRS homologues from Thermotoga maritima, TM1875 and TM1351, have been biochemically characterized and it has been clarified that only TM1875 functions as an ND-GluRS. Furthermore, the crystal structure of the T. maritima ND-GluRS, TM1875, was determined in complex with a Glu-AMP analogue at 2.0 A resolution. The T. maritima ND-GluRS contains a characteristic structure in the connective-peptide domain, which is inserted into the catalytic Rossmann-fold domain. The glutamylation ability of tRNA(Gln) by ND-GluRS was measured in the presence of the bacterial Glu-tRNA(Gln) amidotransferase GatCAB. Interestingly, the glutamylation efficiency was not affected even in the presence of excess GatCAB. Therefore, GluRS avoids competition with GatCAB and glutamylates tRNA(Gln).


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamyl-tRNA synthetase 2
A
488Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: gltX2
EC: 6.1.1.17
Find proteins for Q9X2I8 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X2I8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSU
Query on GSU

Download SDF File 
Download CCD File 
A
O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE
C15 H21 N7 O9 S
YBRKRYFZKHICLS-WERHYGNASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.624α = 90.00
b = 207.317β = 90.00
c = 39.495γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
CNSrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-03-01 
  • Released Date: 2010-06-30 
  • Deposition Author(s): Ito, T., Yokoyama, S.

Revision History 

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance