7POZ | pdb_00007poz

Crystal structure of Schistosoma mansoni HDAC8 with DMSO bound in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.212 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7POZ

This is version 1.2 of the entry. See complete history

Literature

Crystal structures of Schistosoma mansoni histone deacetylase 8 reveal a novel binding site for allosteric inhibitors.

Saccoccia, F.Pozzetti, L.Gimmelli, R.Butini, S.Guidi, A.Papoff, G.Giannaccari, M.Brogi, S.Scognamiglio, V.Gemma, S.Ruberti, G.Campiani, G.

(2022) J Biological Chem 298: 102375-102375

  • DOI: https://doi.org/10.1016/j.jbc.2022.102375
  • Primary Citation Related Structures: 
    7P2S, 7P2T, 7P2U, 7P2V, 7POZ

  • PubMed Abstract: 

    Parasitic diseases cause significant global morbidity and mortality particularly in the poorest regions of the world. Schistosomiasis, one of the most widespread neglected tropical diseases, affects more than 200 million people worldwide. Histone deacetylase (HDAC) inhibitors are prominent epigenetic drugs that are being investigated in the treatment of several diseases, including cancers and parasitic diseases. Schistosoma mansoni HDAC8 (SmHDAC8) is highly expressed in all life cycle stages of the parasite, and selective inhibition is required in order to avoid undesirable off-target effects in the host. Herein, by X-ray crystal structures of SmHDAC8-inhibitor complexes, biochemical and phenotypic studies, we found two schistosomicidal spiroindoline derivatives binding a novel site, next to Trp198, on the enzyme surface. We determined that by acting on this site, either by mutation of the Trp198 or by compound binding, a decrease in the activity of the enzyme is achieved. Remarkably, this allosteric site differs from the human counterpart; rather, it is conserved in all Schistosoma species, as well as Rhabidoptera and Trematoda classes, thus paving the way for the design of HDAC8-selective allosteric inhibitors with improved properties.


  • Organizational Affiliation
    • Institute of Biochemistry and Cell Biology, Italian National Research Council (IBBC-CNR), Adriano Buzzati-Traverso Campus, Monterotondo Scalo, Rome, Italy. Electronic address: fulvio.saccoccia@cnr.it.

Macromolecule Content 

  • Total Structure Weight: 50.15 kDa 
  • Atom Count: 3,485 
  • Modeled Residue Count: 405 
  • Deposited Residue Count: 440 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone deacetylase 8440Schistosoma mansoniMutation(s): 0 
Gene Names: HDAC8
EC: 3.5.1.98
UniProt
Find proteins for A5H660 (Schistosoma mansoni)
Explore A5H660 
Go to UniProtKB:  A5H660
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5H660
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.212 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.738α = 90
b = 70.738β = 90
c = 179.462γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description