1G59

GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU).


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
TRNA(GLU)A [auth B],
B [auth D]
75N/A
Protein Feature View
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  • Reference Sequence
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 = 109.98α = 90
b = 218.67β = 90
c = 134.67γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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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