Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

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This is version 1.4 of the entry. See complete history


L-arginine recognition by yeast arginyl-tRNA synthetase.

Cavarelli, J.Delagoutte, B.Eriani, G.Gangloff, J.Moras, D.

(1998) EMBO J 17: 5438-5448

  • DOI: https://doi.org/10.1093/emboj/17.18.5438
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of arginyl-tRNA synthetase (ArgRS) from Saccharomyces cerevisiae, a class I aminoacyl-tRNA synthetase (aaRS), with L-arginine bound to the active site has been solved at 2.75 A resolution and refined to a crystallographic R-factor of 19.7%. ArgRS is composed predominantly of alpha-helices and can be divided into five domains, including the class I-specific active site. The N-terminal domain shows striking similarity to some completely unrelated proteins and defines a module which should participate in specific tRNA recognition. The C-terminal domain, which is the putative anticodon-binding module, displays an all-alpha-helix fold highly similar to that of Escherichia coli methionyl-tRNA synthetase. While ArgRS requires tRNAArg for the first step of the aminoacylation reaction, the results show that its presence is not a prerequisite for L-arginine binding. All H-bond-forming capability of L-arginine is used by the protein for the specific recognition. The guanidinium group forms two salt bridge interactions with two acidic residues, and one H-bond with a tyrosine residue; these three residues are strictly conserved in all ArgRS sequences. This tyrosine is also conserved in other class I aaRS active sites but plays several functional roles. The ArgRS structure allows the definition of a new framework for sequence alignments and subclass definition in class I aaRSs.

  • Organizational Affiliation

    UPR 9004 Biologie Structurale, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (ARGINYL-TRNA SYNTHETASE)607Saccharomyces cerevisiaeMutation(s): 0 
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ARG

Download Ideal Coordinates CCD File 
C6 H15 N4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.374α = 90
b = 100.374β = 90
c = 204.341γ = 90
Software Package:
Software NamePurpose
CCP4model building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-27
    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: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations