4UP7

Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase in complex with lysyl-adenylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of Entamoeba Histolytica Lysyl-tRNA Synthetase Reveal Conformational Changes Upon Lysine Binding and a Specific Helix Bundle Domain.

Bonnefond, L.Castro De Moura, M.Ribas De Pouplana, L.Nureki, O.

(2014) FEBS Lett 588: 4478

  • DOI: 10.1016/j.febslet.2014.10.019
  • Primary Citation of Related Structures:  
    4UPA, 4UP7, 4UP8, 4UP9

  • PubMed Abstract: 
  • The class II lysyl-tRNA synthetases (KRS) are conserved aminoacyl-tRNA synthetases that attach lysine to the cognate tRNA in a two-step mechanism. The enzyme from the parasitic protozoan Entamoeba histolytica was crystallized in the presence of small ...

    The class II lysyl-tRNA synthetases (KRS) are conserved aminoacyl-tRNA synthetases that attach lysine to the cognate tRNA in a two-step mechanism. The enzyme from the parasitic protozoan Entamoeba histolytica was crystallized in the presence of small ligands to generate snapshots of the lysine-adenylate formation. The residues involved in lysine activation are highly conserved and the active site closes around the lysyl-adenylate, as observed in bacterial KRS. The Entamoeba EMAPII-like polypeptide is not resolved in the crystals, but another Entamoeba-specific insertion could be modeled as a small helix bundle that may contribute to tRNA binding through interaction with the tRNA hinge.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16, Yayoi, Bunkyo, Tokyo 113-0032, Japan. lbonnefond@unistra.fr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSINE--TRNA LIGASEA777Entamoeba histolyticaMutation(s): 1 
Gene Names: EHI_047810
EC: 6.1.1.6
Find proteins for C4M7X2 (Entamoeba histolytica)
Explore C4M7X2 
Go to UniProtKB:  C4M7X2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAD
Query on LAD

Download CCD File 
A
ADENOSINE-5'-[LYSYL-PHOSPHATE]
C16 H26 N7 O8 P
RZWIOOBQBMRZTQ-OPYVMVOTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.765α = 90
b = 155.765β = 90
c = 95.292γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 1.2: 2014-11-26
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Database references