1F7U

CRYSTAL STRUCTURE OF THE ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNA(ARG) AND L-ARG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding

Delagoutte, B., Moras, D., Cavarelli, J.

(2000) EMBO J 19: 5599-5610

  • DOI: https://doi.org/10.1093/emboj/19.21.5599
  • Primary Citation of Related Structures:  
    1F7U, 1F7V

  • PubMed Abstract: 

    • The 2.2 A crystal structure of a ternary complex formed by yeast arginyl-tRNA synthetase and its cognate tRNA(Arg) in the presence of the L-arginine substrate highlights new atomic features used for specific substrate recognition. This first example of an active complex formed by a class Ia aminoacyl-tRNA synthetase and its natural cognate tRNA illustrates additional strategies used for specific tRNA selection ...

    The 2.2 A crystal structure of a ternary complex formed by yeast arginyl-tRNA synthetase and its cognate tRNA(Arg) in the presence of the L-arginine substrate highlights new atomic features used for specific substrate recognition. This first example of an active complex formed by a class Ia aminoacyl-tRNA synthetase and its natural cognate tRNA illustrates additional strategies used for specific tRNA selection. The enzyme specifically recognizes the D-loop and the anticodon of the tRNA, and the mutually induced fit produces a conformation of the anticodon loop never seen before. Moreover, the anticodon binding triggers conformational changes in the catalytic center of the protein. The comparison with the 2.9 A structure of a binary complex formed by yeast arginyl-tRNA synthetase and tRNA(Arg) reveals that L-arginine binding controls the correct positioning of the CCA end of the tRNA(Arg). Important structural changes induced by substrate binding are observed in the enzyme. Several key residues of the active site play multiple roles in the catalytic pathway and thus highlight the structural dynamics of the aminoacylation reaction.

    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNA complexes
      Delagoutte, B., Keith, G., Moras, D., Cavarelli, J.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 492
    Organizational Affiliation: 

    UPR 9004 Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France. cava@igbmc.u-strasbg.fr



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ARGINYL-TRNA SYNTHETASEB [auth A]607Saccharomyces cerevisiaeMutation(s): 0 
EC: 6.1.1.19
UniProt
Find proteins for Q05506 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05506 
Go to UniProtKB:  Q05506
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05506
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
TRNA(ARG)A [auth B]76N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG
Download Ideal Coordinates CCD File 
D [auth A]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.646α = 90
b = 107.472β = 90
c = 71.379γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance