7Q1C

Crystal structure of Trypanosoma cruzi histone deacetylase DAC2 complexed with a hydroxamate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Species-selective targeting of pathogens revealed by the atypical structure and active site of Trypanosoma cruzi histone deacetylase DAC2.

Marek, M.Ramos-Morales, E.Picchi-Constante, G.F.A.Bayer, T.Norstrom, C.Herp, D.Sales-Junior, P.A.Guerra-Slompo, E.P.Hausmann, K.Chakrabarti, A.Shaik, T.B.Merz, A.Troesch, E.Schmidtkunz, K.Goldenberg, S.Pierce, R.J.Mourao, M.M.Jung, M.Schultz, J.Sippl, W.Zanchin, N.I.T.Romier, C.

(2021) Cell Rep 37: 110129-110129

  • DOI: https://doi.org/10.1016/j.celrep.2021.110129
  • Primary Citation of Related Structures:  
    7Q1B, 7Q1C

  • PubMed Abstract: 

    Writing and erasing of posttranslational modifications are crucial to phenotypic plasticity and antigenic variation of eukaryotic pathogens. Targeting pathogens' modification machineries, thus, represents a valid approach to fighting parasitic diseases. However, identification of parasitic targets and the development of selective anti-parasitic drugs still represent major bottlenecks. Here, we show that the zinc-dependent histone deacetylases (HDACs) of the protozoan parasite Trypanosoma cruzi are key regulators that have significantly diverged from their human counterparts. Depletion of T. cruzi class I HDACs tcDAC1 and tcDAC2 compromises cell-cycle progression and division, leading to cell death. Notably, tcDAC2 displays a deacetylase activity essential to the parasite and shows major structural differences with human HDACs. Specifically, tcDAC2 harbors a modular active site with a unique subpocket targeted by inhibitors showing substantial anti-parasitic effects in cellulo and in vivo. Thus, the targeting of the many atypical HDACs in pathogens can enable anti-parasitic selective chemical impairment.


  • Organizational Affiliation

    Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, U 1258, 67404 Illkirch, France; IGBMC, Department of Integrated Structural Biology, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase DAC2
A, B
467Trypanosoma cruziMutation(s): 0 
UniProt
Find proteins for A0A1B1JH81 (Trypanosoma cruzi)
Explore A0A1B1JH81 
Go to UniProtKB:  A0A1B1JH81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B1JH81
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T56 (Subject of Investigation/LOI)
Query on T56

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
(E)-3-dibenzofuran-4-yl-N-oxidanyl-prop-2-enamide
C15 H11 N O3
KLEYDFVKAXXYIY-CMDGGOBGSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.071α = 90
b = 95.353β = 103.501
c = 96.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Communitys Seventh Framework ProgrammeEuropean Union602080

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description