3I7F

Aspartyl tRNA synthetase from Entamoeba histolytica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the aspartyl-tRNA synthetase from Entamoeba histolytica.

Merritt, E.A.Arakaki, T.L.Larson, E.T.Kelley, A.Mueller, N.Napuli, A.J.Zhang, L.Deditta, G.Luft, J.Verlinde, C.L.Fan, E.Zucker, F.Buckner, F.S.Van Voorhis, W.C.Hol, W.G.

(2010) Mol.Biochem.Parasitol. 169: 95-100

  • DOI: 10.1016/j.molbiopara.2009.10.005

  • PubMed Abstract: 
  • The crystal structure of the aspartyl-tRNA synthetase from the eukaryotic parasite Entamoeba histolytica has been determined at 2.8Aresolution. Relative to homologous sequences, the E. histolytica protein contains a 43-residue insertion between the N ...

    The crystal structure of the aspartyl-tRNA synthetase from the eukaryotic parasite Entamoeba histolytica has been determined at 2.8Aresolution. Relative to homologous sequences, the E. histolytica protein contains a 43-residue insertion between the N-terminal anticodon binding domain and the C-terminal catalytic domain. The present structure reveals that this insertion extends an arm of the hinge region that has previously been shown to mediate interaction of aspartyl-tRNA synthetase with the cognate tRNA D-stem. Modeling indicates that this Entamoeba-specific insertion is likely to increase the interaction surface with the cognate tRNA(Asp). In doing so it may substitute functionally for an RNA-binding motif located in N-terminal extensions found in AspRS sequences from lower eukaryotes but absent in Entamoeba. The E. histolytica AspRS structure shows a well-ordered N-terminus that contributes to the AspRS dimer interface.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Mailstop 357742, Seattle, WA 98195, USA. merritt@u.washington.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartyl-tRNA synthetase
A, B
548Entamoeba histolyticaMutation(s): 0 
Find proteins for C4LZN0 (Entamoeba histolytica)
Go to UniProtKB:  C4LZN0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 247.848α = 90.00
b = 247.848β = 90.00
c = 56.295γ = 120.00
Software Package:
Software NamePurpose
BALBESphasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description