4YV0

Crystal structure of Trypanosoma cruzi spermidine synthase in complex with (2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine- 2-carboxamid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural insights into the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase

Amano, Y.Namatame, I.Tateishi, Y.Honboh, K.Tanabe, E.Niimi, T.Sakashita, H.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1879-1889

  • DOI: https://doi.org/10.1107/S1399004715013048
  • Primary Citation of Related Structures:  
    4YUV, 4YUW, 4YUX, 4YUY, 4YUZ, 4YV0, 4YV1, 4YV2

  • PubMed Abstract: 

    Trypanosoma cruzi causes Chagas disease, a severe disease affecting 8-10 million people in Latin America. While nifurtimox and benznidazole are used to treat this disease, their efficacy is limited and adverse effects are observed. New therapeutic targets and novel drugs are therefore urgently required. Enzymes in the polyamine-trypanothione pathway are promising targets for the treatment of Chagas disease. Spermidine synthase is a key enzyme in this pathway that catalyzes the transfer of an aminopropyl group from decarboxylated S-adenosylmethionine (dcSAM) to putrescine. Fragment-based drug discovery was therefore conducted to identify novel, potent inhibitors of spermidine synthase from T. cruzi (TcSpdSyn). Here, crystal structures of TcSpdSyn in complex with dcSAM, trans-4-methylcyclohexylamine and hit compounds from fragment screening are reported. The structure of dcSAM complexed with TcSpdSyn indicates that dcSAM stabilizes the conformation of the `gatekeeping' loop to form the putrescine-binding pocket. The structures of fragments bound to TcSpdSyn revealed two fragment-binding sites: the putrescine-binding pocket and the dimer interface. The putrescine-binding pocket was extended by an induced-fit mechanism. The crystal structures indicate that the conformation of the dimer interface is required to stabilize the gatekeeping loop and that fragments binding to this interface inhibit TcSpdSyn by disrupting its conformation. These results suggest that utilizing the dynamic structural changes in TcSpdSyn that occur upon inhibitor binding will facilitate the development of more selective and potent inhibitors.


  • Organizational Affiliation

    Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine synthase, putative
A, B, C, D
304Trypanosoma cruzi strain CL BrenerMutation(s): 0 
Gene Names: Tc00.1047053510339.50
EC: 2.5.1.16
UniProt
Find proteins for Q4DA73 (Trypanosoma cruzi (strain CL Brener))
Explore Q4DA73 
Go to UniProtKB:  Q4DA73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4DA73
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.56α = 90
b = 99.783β = 90.64
c = 135.005γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Structure summary
  • Version 1.2: 2020-02-05
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description