1F7V | pdb_00001f7v

CRYSTAL STRUCTURE OF YEAST ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNAARG

• PDB DOI: https://doi.org/10.2210/pdb1F7V/pdb
• NAKB: 1F7V

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


• Deposited: 2000-06-28 Released: 2001-06-27 
• Deposition Author(s): Delagoutte, B., Moras, D., Cavarelli, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.245 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

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

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

(2000) EMBO J 19: 5599-5610

• PubMed: 11060012 
• DOI: https://doi.org/10.1093/emboj/19.21.5599
• Primary Citation 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 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.

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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. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.19 kDa 
• Atom Count: 6,503 
• Modeled Residue Count: 679 
• Deposited Residue Count: 683 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARGINYL-TRNA SYNTHETASE	B [auth A]	607	Saccharomyces cerevisiae	Mutation(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 ID: 1
Molecule	Chains	Length	Organism	Image
TRNA(ARG)	A [auth B]	76	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.245 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.721	α = 90
b = 129.606	β = 90
c = 184.006	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-06-27 
Deposition Author(s): Delagoutte, B., Moras, D., Cavarelli, J.

Revision History  

• 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
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations