Aspartyl tRNA synthetase from Entamoeba histolytica

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1016/j.molbiopara.2009.10.005
  • Primary Citation of Related Structures:  

  • 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-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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartyl-tRNA synthetase
A, B
548Entamoeba histolyticaMutation(s): 0 
Gene Names: EHI_175050
Find proteins for C4LZN0 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
Explore C4LZN0 
Go to UniProtKB:  C4LZN0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4LZN0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 247.848α = 90
b = 247.848β = 90
c = 56.295γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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