6MYL

The Prp8 intein-cisplatin complex

  • Classification: hydrolase/hydrolase inhibitor
  • Organism(s): Cryptococcus deuterogattii R265
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-11-01 Released: 2019-11-06 
  • Deposition Author(s): Li, Z., Li, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cisplatin protects mice from challenge ofCryptococcus neoformansby targeting the Prp8 intein.

Li, Z.Fu, B.Green, C.M.Liu, B.Zhang, J.Lang, Y.Chaturvedi, S.Belfort, M.Liao, G.Li, H.

(2019) Emerg Microbes Infect 8: 895-908

  • DOI: https://doi.org/10.1080/22221751.2019.1625727
  • Primary Citation of Related Structures:  
    6MWY, 6MYL

  • PubMed Abstract: 

    The Prp8 intein is one of the most widespread eukaryotic inteins, present in important pathogenic fungi, including Cryptococcus and Aspergillus species. Because the processed Prp8 carries out essential and non-redundant cellular functions, a Prp8 intein inhibitor is a mechanistically novel antifungal agent. In this report, we demonstrated that cisplatin, an FDA-approved cancer drug, significantly arrested growth of Prp8 intein-containing fungi C. neoformans and C. gattii, but only poorly inhibited growth of intein-free Candida species. These results suggest that cisplatin arrests fungal growth through specific inhibition of the Prp8 intein. Cisplatin was also found to significantly inhibit growth of C. neoformans in a mouse model. Our results further showed that cisplatin inhibited Prp8 intein splicing in vitro in a dose-dependent manner by direct binding to the Prp8 intein. Crystal structures of the apo- and cisplatin-bound Prp8 inteins revealed that two degenerate cisplatin molecules bind at the intein active site. Mutation of the splicing-site residues led to loss of cisplatin binding, as well as impairment of intein splicing. Finally, we found that overexpression of the Prp8 intein in cryptococcal species conferred cisplatin resistance. Overall, these results indicate that the Prp8 intein is a novel antifungal target worth further investigation.


  • Organizational Affiliation

    New York State Department of Health , Wadsworth Center, Albany, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8
A, B, C
214Cryptococcus deuterogattii R265Mutation(s): 0 
Gene Names: CNBG_0411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.248 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.853α = 90
b = 74.853β = 90
c = 191.886γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2019-11-06 
  • Deposition Author(s): Li, Z., Li, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM39422
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM44844
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI140726-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2020-05-20
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection