1G59 | pdb_00001g59

GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.298 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1G59

This is version 1.3 of the entry. See complete history

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

  • DOI: https://doi.org/10.1038/84927
  • Primary Citation 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'.


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

Macromolecule Content 

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

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUTAMYL-TRNA SYNTHETASEC [auth A],
D [auth C]
468Thermus thermophilusMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27000
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
TRNA(GLU)A [auth B],
B [auth D]
75N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.298 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.98α = 90
b = 218.67β = 90
c = 134.67γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-08-02
    Changes: Database references, Refinement description