5EAD

Saccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor S-desthio-prothioconazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Functional Elucidation of Yeast Lanosterol 14 alpha-Demethylase in Complex with Agrochemical Antifungals.

Tyndall, J.D.Sabherwal, M.Sagatova, A.A.Keniya, M.V.Negroni, J.Wilson, R.K.Woods, M.A.Tietjen, K.Monk, B.C.

(2016) PLoS One 11: e0167485-e0167485

  • DOI: 10.1371/journal.pone.0167485
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Azole antifungals, known as demethylase inhibitors (DMIs), target sterol 14α-demethylase (CYP51) in the ergosterol biosynthetic pathway of fungal pathogens of both plants and humans. DMIs remain the treatment of choice in crop protection against a wi ...

    Azole antifungals, known as demethylase inhibitors (DMIs), target sterol 14α-demethylase (CYP51) in the ergosterol biosynthetic pathway of fungal pathogens of both plants and humans. DMIs remain the treatment of choice in crop protection against a wide range of fungal phytopathogens that have the potential to reduce crop yields and threaten food security. We used a yeast membrane protein expression system to overexpress recombinant hexahistidine-tagged S. cerevisiae lanosterol 14α-demethylase and the Y140F or Y140H mutants of this enzyme as surrogates in order characterize interactions with DMIs. The whole-cell antifungal activity (MIC50 values) of both the R- and S-enantiomers of tebuconazole, prothioconazole (PTZ), prothioconazole-desthio, and oxo-prothioconazole (oxo-PTZ) as well as for fluquinconazole, prochloraz and a racemic mixture of difenoconazole were determined. In vitro binding studies with the affinity purified enzyme were used to show tight type II binding to the yeast enzyme for all compounds tested except PTZ and oxo-PTZ. High resolution X-ray crystal structures of ScErg11p6×His in complex with seven DMIs, including four enantiomers, reveal triazole-mediated coordination of all compounds and the specific orientation of compounds within the relatively hydrophobic binding site. Comparison with CYP51 structures from fungal pathogens including Candida albicans, Candida glabrata and Aspergillus fumigatus provides strong evidence for a highly conserved CYP51 structure including the drug binding site. The structures obtained using S. cerevisiae lanosterol 14α-demethylase in complex with these agrochemicals provide the basis for understanding the impact of mutations on azole susceptibility and a platform for the structure-directed design of the next-generation of DMIs.


    Related Citations: 
    • Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14alpha-Demethylase.
      Sagatova, A.A., Keniya, M.V., Wilson, R.K., Monk, B.C., Tyndall, J.D.
      (2015) Antimicrob Agents Chemother 59: 4982

    Organizational Affiliation

    Department of Oral Sciences, New Zealand's National Centre for Dentistry, University of Otago, Dunedin, New Zealand.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lanosterol 14-alpha demethylase
A
539Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ERG11SCY_2394
Membrane protein
inferred by homology
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Cytochromes P450
Protein: 
Lanosterol 14α-demethylase with bound lanosterol
Find proteins for A6ZSR0 (Saccharomyces cerevisiae (strain YJM789))
Go to UniProtKB:  A6ZSR0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
5L9
Query on 5L9

Download CCD File 
A
(2~{S})-2-(1-chloranylcyclopropyl)-1-(2-chlorophenyl)-3-(1,2,4-triazol-1-yl)propan-2-ol
C14 H15 Cl2 N3 O
HHUQPWODPBDTLI-AWEZNQCLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.27α = 90
b = 67.18β = 99.09
c = 80.91γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bayer CropScienceGermany--

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references