4BZ6

Crystal structure of Schistosoma mansoni HDAC8 complexed with SAHA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for the Inhibition of Histone Deacetylase 8 (Hdac8), a Key Epigenetic Player in the Blood Fluke Schistosoma Mansoni.

Marek, M.Kannan, S.Hauser, A.Moraes Mourao, M.Caby, S.Cura, V.Stolfa, D.A.Schmidtkunz, K.Lancelot, J.Andrade, L.Renaud, J.Oliveira, G.Sippl, W.Jung, M.Cavarelli, J.Pierce, R.J.Romier, C.

(2013) Plos Pathog. 9: 03645

  • DOI: 10.1371/journal.ppat.1003645
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The treatment of schistosomiasis, a disease caused by blood flukes parasites of the Schistosoma genus, depends on the intensive use of a single drug, praziquantel, which increases the likelihood of the development of drug-resistant parasite strains a ...

    The treatment of schistosomiasis, a disease caused by blood flukes parasites of the Schistosoma genus, depends on the intensive use of a single drug, praziquantel, which increases the likelihood of the development of drug-resistant parasite strains and renders the search for new drugs a strategic priority. Currently, inhibitors of human epigenetic enzymes are actively investigated as novel anti-cancer drugs and have the potential to be used as new anti-parasitic agents. Here, we report that Schistosoma mansoni histone deacetylase 8 (smHDAC8), the most expressed class I HDAC isotype in this organism, is a functional acetyl-L-lysine deacetylase that plays an important role in parasite infectivity. The crystal structure of smHDAC8 shows that this enzyme adopts a canonical α/β HDAC fold, with specific solvent exposed loops corresponding to insertions in the schistosome HDAC8 sequence. Importantly, structures of smHDAC8 in complex with generic HDAC inhibitors revealed specific structural changes in the smHDAC8 active site that cannot be accommodated by human HDACs. Using a structure-based approach, we identified several small-molecule inhibitors that build on these specificities. These molecules exhibit an inhibitory effect on smHDAC8 but show reduced affinity for human HDACs. Crucially, we show that a newly identified smHDAC8 inhibitor has the capacity to induce apoptosis and mortality in schistosomes. Taken together, our biological and structural findings define the framework for the rational design of small-molecule inhibitors specifically interfering with schistosome epigenetic mechanisms, and further support an anti-parasitic epigenome targeting strategy to treat neglected diseases caused by eukaryotic pathogens.


    Organizational Affiliation

    Département de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTONE DEACETYLASE 8
A, B, C, D
446Schistosoma mansoniMutation(s): 0 
Gene Names: HDAC8
EC: 3.5.1.98
Find proteins for A5H660 (Schistosoma mansoni)
Go to Gene View: HDAC8
Go to UniProtKB:  A5H660
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMF
Query on DMF

Download SDF File 
Download CCD File 
B, C
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
SHH
Query on SHH

Download SDF File 
Download CCD File 
A, B, C, D
OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE
SAHA
C14 H20 N2 O3
WAEXFXRVDQXREF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.163 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 70.640α = 77.88
b = 70.640β = 75.48
c = 97.990γ = 85.69
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-07-24 
  • Released Date: 2013-08-14 
  • Deposition Author(s): Marek, M., Romier, C.

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references