6GXG

Tryparedoxin from Trypanosoma brucei in complex with CFT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Inhibitor-Induced Dimerization of an Essential Oxidoreductase from African Trypanosomes.

Wagner, A.Le, T.A.Brennich, M.Klein, P.Bader, N.Diehl, E.Paszek, D.Weickhmann, A.K.Dirdjaja, N.Krauth-Siegel, R.L.Engels, B.Opatz, T.Schindelin, H.Hellmich, U.A.

(2019) Angew Chem Int Ed Engl 58: 3640-3644

  • DOI: https://doi.org/10.1002/anie.201810470
  • Primary Citation of Related Structures:  
    6GXG, 6GXY

  • PubMed Abstract: 

    Trypanosomal and leishmanial infections claim tens of thousands of lives each year. The metabolism of these unicellular eukaryotic parasites differs from the human host and their enzymes thus constitute promising drug targets. Tryparedoxin (Tpx) from Trypanosoma brucei is the essential oxidoreductase in the parasite's hydroperoxide-clearance cascade. In vitro and in vivo functional assays show that a small, selective inhibitor efficiently inhibits Tpx. With X-ray crystallography, SAXS, analytical SEC, SEC-MALS, MD simulations, ITC, and NMR spectroscopy, we show how covalent binding of this monofunctional inhibitor leads to Tpx dimerization. Intra- and intermolecular inhibitor-inhibitor, protein-protein, and inhibitor-protein interactions stabilize the dimer. The behavior of this efficient antitrypanosomal molecule thus constitutes an exquisite example of chemically induced dimerization with a small, monovalent ligand that can be exploited for future drug design.


  • Organizational Affiliation

    Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Johann-Joachim-Becherweg 31, 55128, Mainz, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryparedoxin145Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for O77404 (Trypanosoma brucei brucei)
Explore O77404 
Go to UniProtKB:  O77404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO77404
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tryparedoxin
B, C
147Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for O77404 (Trypanosoma brucei brucei)
Explore O77404 
Go to UniProtKB:  O77404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO77404
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.68α = 90
b = 95.736β = 96.61
c = 48.043γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description