1BBU

LYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1021/bi001487r
  • Primary Citation of Related Structures:  
    1BBW, 1BBU

  • 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 ...

    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.


    Related Citations: 
    • Crystal Structure of the Lysyl-tRNA Synthetase (Lysu) from Escherichia Coli
      Onesti, S., Miller, A.D., Brick, P.
      (1995) Structure 3: 163
    • Comparison of the Enzymatic Properties of Two Escherichia Coli Lysyl-tRNA Synthetase Species
      Brevet, A., Chen, J., Leveque, F., Blanquet, S., Plateau, P.
      (1995) J Biol Chem 270: 14439

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (LYSYL-TRNA SYNTHETASE)A504Escherichia coli K-12Mutation(s): 0 
Gene Names: lysSasuDherCb2890JW2858
EC: 6.1.1.6
UniProt
Find proteins for P0A8N3 (Escherichia coli (strain K12))
Explore P0A8N3 
Go to UniProtKB:  P0A8N3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download Ideal Coordinates CCD File 
B [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.82α = 90
b = 181.82β = 90
c = 93.07γ = 120
Software Package:
Software NamePurpose
CCP4model building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing

Structure Validation

View Full Validation Report



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