4UPA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.901 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.4 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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE--TRNA LIGASE
A
777Entamoeba histolyticaMutation(s): 1 
EC: 6.1.1.6
Find proteins for C4M7X2 (Entamoeba histolytica)
Go to UniProtKB:  C4M7X2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.901 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 156.820α = 90.00
b = 156.820β = 90.00
c = 94.132γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-11-05
    Type: Database references
  • Version 1.2: 2014-11-26
    Type: Database references
  • Version 1.3: 2014-12-10
    Type: Database references
  • Version 1.4: 2015-02-11
    Type: Data collection