Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 

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Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.

Onesti, S.Desogus, G.Brevet, A.Chen, J.Plateau, P.Blanquet, S.Brick, P.

(2000) Biochemistry 39: 12853-12861

  • DOI: https://doi.org/10.1021/bi001487r
  • Primary Citation of Related Structures:  
    1BBU, 1BBW

  • PubMed Abstract: 

    Lysyl-tRNA synthetase is a member of the class II aminoacyl-tRNA synthetases and catalyses the specific aminoacylation of tRNA(Lys). The crystal structure of the constitutive lysyl-tRNA synthetase (LysS) from Escherichia coli has been determined to 2.7 A resolution in the unliganded form and in a complex with the lysine substrate. A comparison between the unliganded and lysine-bound structures reveals major conformational changes upon lysine binding. The lysine substrate is involved in a network of hydrogen bonds. Two of these interactions, one between the alpha-amino group and the carbonyl oxygen of Gly 216 and the other between the carboxylate group and the side chain of Arg 262, trigger a subtle and complicated reorganization of the active site, involving the ordering of two loops (residues 215-217 and 444-455), a change in conformation of residues 393-409, and a rotation of a 4-helix bundle domain (located between motif 2 and 3) by 10 degrees. The result of these changes is a closing up of the active site upon lysine binding.

  • Organizational Affiliation

    Biophysics Section, Blackett Laboratory, Imperial College, London SW7 2BZ, UK. s.onesti@ic.ac.uk

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (LYSYL-TRNA SYNTHETASE)504Escherichia coli K-12Mutation(s): 0 
Gene Names: LYSS
Find proteins for P0A8N3 (Escherichia coli (strain K12))
Explore P0A8N3 
Go to UniProtKB:  P0A8N3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8N3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.936α = 90
b = 182.936β = 90
c = 92.516γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
CCP4model building
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Refinement description