8BPT

Crystal structure of the second bromodomain of BRD5 from Leishmania donovani


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery.

Russell, C.N.Carter, J.L.Borgia, J.M.Bush, J.Calderon, F.Gabarro, R.Conway, S.J.Mottram, J.C.Wilkinson, A.J.Jones, N.G.

(2023) ACS Infect Dis 9: 2340-2357

  • DOI: https://doi.org/10.1021/acsinfecdis.3c00431
  • Primary Citation of Related Structures:  
    8BPT

  • PubMed Abstract: 

    Leishmaniases are a collection of neglected tropical diseases caused by kinetoplastid parasites in the genus Leishmania . Current chemotherapies are severely limited, and the need for new antileishmanials is of pressing international importance. Bromodomains are epigenetic reader domains that have shown promising therapeutic potential for cancer therapy and may also present an attractive target to treat parasitic diseases. Here, we investigate Leishmania donovani bromodomain factor 5 ( Ld BDF5) as a target for antileishmanial drug discovery. Ld BDF5 contains a pair of bromodomains (BD5.1 and BD5.2) in an N-terminal tandem repeat. We purified recombinant bromodomains of L. donovani BDF5 and determined the structure of BD5.2 by X-ray crystallography. Using a histone peptide microarray and fluorescence polarization assay, we identified binding interactions of Ld BDF5 bromodomains with acetylated peptides derived from histones H2B and H4. In orthogonal biophysical assays including thermal shift assays, fluorescence polarization, and NMR, we showed that BDF5 bromodomains bind to human bromodomain inhibitors SGC-CBP30, bromosporine, and I-BRD9; moreover, SGC-CBP30 exhibited activity against Leishmania promastigotes in cell viability assays. These findings exemplify the potential BDF5 holds as a possible drug target in Leishmania and provide a foundation for the future development of optimized antileishmanial compounds targeting this epigenetic reader protein.


  • Organizational Affiliation

    York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromo domain-containing protein
A, B
140Leishmania donovani BPK282A1Mutation(s): 0 
Gene Names: LDBPK_091320
UniProt
Find proteins for A0A3Q8I8I6 (Leishmania donovani)
Explore A0A3Q8I8I6 
Go to UniProtKB:  A0A3Q8I8I6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q8I8I6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.37α = 90
b = 75.356β = 90
c = 105.798γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
pointlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/P027989/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomWhite Rose DTP

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Database references