1GLN

ARCHITECTURES OF CLASS-DEFINING AND SPECIFIC DOMAINS OF GLUTAMYL-TRNA SYNTHETASE

• PDB DOI: https://doi.org/10.2210/pdb1GLN/pdb

• Classification: AMINOACYL-TRNA SYNTHASE
• Organism(s): Thermus thermophilus HB8
• Mutation(s): No 


• Deposited: 1994-07-20 Released: 1995-10-15 
• Deposition Author(s): Nureki, O., Vassylyev, D.G., Katayanagi, K., Shimizu, T., Sekine, S., Kigawa, T., Miyazawa, T., Yokoyama, S., Morikawa, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Literature

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: 1958-1965

• PubMed: 7701318 
• DOI: https://doi.org/10.1126/science.7701318
• Primary Citation of Related Structures:  
  1GLN


• PubMed Abstract: 
  

  The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus, was solved and refined at 2.5 A resolution. The amino-terminal half of GluRS shows a geometrical similarity with that of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) of the same subclass in class I, comprising the class I-specific Rossmann fold domain and the intervening subclass-specific alpha/beta domain. These domains were found to have two GluRS-specific, secondary-structure insertions, which then participated in the specific recognition of the D and acceptor stems of tRNA(Glu) as indicated by mutagenesis analyses based on the docking properties of GluRS and tRNA. In striking contrast to the beta-barrel structure of the GlnRS carboxyl-terminal half, the GluRS carboxyl-terminal half displayed an all-alpha-helix architecture, an alpha-helix cage, and mutagenesis analyses indicated that it had a role in the anticodon recognition.

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Organizational Affiliation: 

Department of Biophysics and Biochemistry, School of Science, University of Tokyo, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.98 kDa 
• Atom Count: 3,973 
• Modelled Residue Count: 468 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMYL-TRNA SYNTHETASE	A	468	Thermus thermophilus HB8	Mutation(s): 0  EC: 6.1.1.17
UniProt
Find proteins for P27000 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P27000  Go to UniProtKB:  P27000

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.75	α = 90
b = 110.09	β = 90
c = 67.56	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-10-15 
Deposition Author(s): Nureki, O., Vassylyev, D.G., Katayanagi, K., Shimizu, T., Sekine, S., Kigawa, T., Miyazawa, T., Yokoyama, S., Morikawa, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 1995-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references