Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 156.17 kDa 
• Atom Count: 11,092 
• Modelled Residue Count: 1,086 
• Deposited Residue Count: 1,086 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 1G59

GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU).

• PDB DOI:  https://doi.org/10.2210/pdb1G59/pdb
• NDB: PR0035

• Classification: LIGASE/RNA
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-10-31 Released: 2001-09-01 
• Deposition Author(s): Sekine, S., Nureki, O., Shimada, A., Vassylyev, D.G., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.298 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Literature

Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase.

Sekine, S., Nureki, O., Shimada, A., Vassylyev, D.G., Yokoyama, S.

(2001) Nat Struct Biol 8: 203-206

• PubMed: 11224561 
• DOI: https://doi.org/10.1038/84927
• Primary Citation of Related Structures:  
  1G59


• PubMed Abstract: 
  

Glutamyl-tRNA synthetases (GluRSs) are divided into two distinct types, with regard to the presence or absence of glutaminyl-tRNA synthetase (GlnRS) in the genetic translation systems. In the original 19-synthetase systems lacking GlnRS, the 'non-discriminating' GluRS glutamylates both tRNAGlu and tRNAGln. In contrast, in the evolved 20-synthetase systems with GlnRS, the 'discriminating' GluRS aminoacylates only tRNAGlu. Here we report the 2.4 A resolution crystal structure of a 'discriminating' GluRS.tRNAGlu complex from Thermus thermophilus. The GluRS recognizes the tRNAGlu anticodon bases via two alpha-helical domains, maintaining the base stacking. We show that the discrimination between the Glu and Gln anticodons (34YUC36 and 34YUG36, respectively) is achieved by a single arginine residue (Arg 358). The mutation of Arg 358 to Gln resulted in a GluRS that does not discriminate between the Glu and Gln anticodons. This change mimics the reverse course of GluRS evolution from anticodon 'non-dicsriminating' to 'discriminating'.

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Organizational Affiliation: 

Cellular Signaling Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMYL-TRNA SYNTHETASE	C [auth A], D [auth C]	468	Thermus thermophilus	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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
TRNA(GLU)	A [auth B], B [auth D]	75	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.298 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.98	α = 90
b = 218.67	β = 90
c = 134.67	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-09-01 
Deposition Author(s): Sekine, S., Nureki, O., Shimada, A., Vassylyev, D.G., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2001-09-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance