3AFH | pdb_00003afh

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

• PDB DOI: https://doi.org/10.2210/pdb3AFH/pdb

• Classification: LIGASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 20606262 
• DOI: https://doi.org/10.1107/S0907444910019086
• Primary Citation Related Structures: 
  3AFH


• 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).

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58 kDa 
• Atom Count: 4,403 
• Modeled Residue Count: 463 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl-tRNA synthetase 2	A	488	Thermotoga maritima	Mutation(s): 0  EC: 6.1.1.17
UniProt
Find proteins for Q9X2I8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X2I8  Go to UniProtKB:  Q9X2I8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSU	B [auth A]	O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE C15 H21 N7 O9 S YBRKRYFZKHICLS-WERHYGNASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.624	α = 90
b = 207.317	β = 90
c = 39.495	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description