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

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

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Structure of nondiscriminating glutamyl-tRNA synthetase from Thermotoga maritima

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

(2010) Acta Crystallogr D Biol Crystallogr 66: 813-820

  • DOI: https://doi.org/10.1107/S0907444910019086
  • Primary Citation of Related Structures:  

  • 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 (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.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamyl-tRNA synthetase 2488Thermotoga maritimaMutation(s): 0 
Find proteins for Q9X2I8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X2I8 
Go to UniProtKB:  Q9X2I8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X2I8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GSU

Download Ideal Coordinates CCD File 
C15 H21 N7 O9 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.624α = 90
b = 207.317β = 90
c = 39.495γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description