5EAH

Saccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor Difenoconazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.541 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 

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
  • Primary Citation of Related Structures:  

  • 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

    Bayer AG, Division Crop Science, Disease Control Research, Monheim, Germany.,Bayer SAS, Division Crop Science, Disease Control Research, Lyon, France.,New Zealand's National School of Pharmacy, University of Otago, Dunedin, New Zealand.,Department of Oral Sciences, New Zealand's National Centre for Dentistry, University of Otago, Dunedin, New Zealand.,Sir John Walsh Research Institute, 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 cerevisiae (strain YJM789)Mutation(s): 0 
Gene Names: ERG11
Find proteins for A6ZSR0 (Saccharomyces cerevisiae (strain YJM789))
Go to UniProtKB:  A6ZSR0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5LW
Query on 5LW

Download SDF File 
Download CCD File 
A
1-[[(2~{S},4~{S})-2-[2-chloranyl-4-(4-chloranylphenoxy)phenyl]-4-methyl-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole
Difenoconazole
C19 H17 Cl2 N3 O3
BQYJATMQXGBDHF-ORAYPTAESA-N
 Ligand Interaction
5LY
Query on 5LY

Download SDF File 
Download CCD File 
A
1-[[(2~{R},4~{R})-2-[2-chloranyl-4-(4-chloranylphenoxy)phenyl]-4-methyl-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole
Difenoconazole
C19 H17 Cl2 N3 O3
BQYJATMQXGBDHF-YJYMSZOUSA-N
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
A
1-[[(2~{R},4~{S})-2-[2-chloranyl-4-(4-chloranylphenoxy)phenyl]-4-methyl-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole
Difenoconazole
C19 H17 Cl2 N3 O3
BQYJATMQXGBDHF-DJJJIMSYSA-N
 Ligand Interaction
5LZ
Query on 5LZ

Download SDF File 
Download CCD File 
A
1-[[(2~{S},4~{R})-2-[2-chloranyl-4-(4-chloranylphenoxy)phenyl]-4-methyl-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole
Difenoconazole
C19 H17 Cl2 N3 O3
BQYJATMQXGBDHF-BFUOFWGJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.541 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.020α = 90.00
b = 67.330β = 98.58
c = 80.900γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references