3HRK

Histidyl-tRNA synthetase from Trypanosoma cruzi (Histidyl-adenylate complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs.

Merritt, E.A.Arakaki, T.L.Gillespie, J.R.Larson, E.T.Kelley, A.Mueller, N.Napuli, A.J.Kim, J.Zhang, L.Verlinde, C.L.Fan, E.Zucker, F.Buckner, F.S.van Voorhis, W.C.Hol, W.G.

(2010) J.Mol.Biol. 397: 481-494

  • DOI: 10.1016/j.jmb.2010.01.051
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of histidyl-tRNA synthetase (HisRS) from the eukaryotic parasites Trypanosoma brucei and Trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme and reveal differences from bacterial homologs. HisRSs i ...

    Crystal structures of histidyl-tRNA synthetase (HisRS) from the eukaryotic parasites Trypanosoma brucei and Trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme and reveal differences from bacterial homologs. HisRSs in general contain an extra domain inserted between conserved motifs 2 and 3 of the Class II aminoacyl-tRNA synthetase catalytic core. The current structures show that the three-dimensional topology of this domain is very different in bacterial and archaeal/eukaryotic forms of the enzyme. Comparison of apo and histidine-bound trypanosomal structures indicates substantial active-site rearrangement upon histidine binding but relatively little subsequent rearrangement after reaction of histidine with ATP to form the enzyme's first reaction product, histidyladenylate. The specific residues involved in forming the binding pocket for the adenine moiety differ substantially both from the previously characterized binding site in bacterial structures and from the homologous residues in human HisRSs. The essentiality of the single HisRS gene in T. brucei is shown by a severe depression of parasite growth rate that results from even partial suppression of expression by RNA interference.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histidyl-tRNA synthetase
A, B
456Trypanosoma cruzi (strain CL Brener)Mutation(s): 0 
EC: 6.1.1.21
Find proteins for Q4DA54 (Trypanosoma cruzi (strain CL Brener))
Go to UniProtKB:  Q4DA54
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAM
Query on HAM

Download SDF File 
Download CCD File 
A, B
HISTIDYL-ADENOSINE MONOPHOSPHATE
C16 H21 N8 O8 P
XTFBSLZFYLGYAT-OPYVMVOTSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 112.360α = 90.00
b = 166.987β = 90.00
c = 66.021γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description