5EAH

Saccharomyces cerevisiae CYP51 complexed with the plant pathogen inhibitor Difenoconazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1371/journal.pone.0167485
  • Primary Citation of Related Structures:  
    5EAB, 5EAC, 5EAD, 5EAE, 5EAF, 5EAG, 5EAH

  • 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 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.


  • Organizational Affiliation

    New Zealand's National School of Pharmacy, University of Otago, Dunedin, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lanosterol 14-alpha demethylase539Saccharomyces cerevisiae YJM789Mutation(s): 0 
Gene Names: ERG11SCY_2394
Membrane Entity: Yes 
UniProt
Find proteins for A6ZSR0 (Saccharomyces cerevisiae (strain YJM789))
Explore A6ZSR0 
Go to UniProtKB:  A6ZSR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6ZSR0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
5LY
Query on 5LY

Download Ideal Coordinates CCD File 
F [auth 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
C19 H17 Cl2 N3 O3
BQYJATMQXGBDHF-YJYMSZOUSA-N
5LX
Query on 5LX

Download Ideal Coordinates CCD File 
E [auth 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
C19 H17 Cl2 N3 O3
BQYJATMQXGBDHF-DJJJIMSYSA-N
5LW
Query on 5LW

Download Ideal Coordinates CCD File 
D [auth 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
C19 H17 Cl2 N3 O3
BQYJATMQXGBDHF-ORAYPTAESA-N
5LZ
Query on 5LZ

Download Ideal Coordinates CCD File 
C [auth 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
C19 H17 Cl2 N3 O3
BQYJATMQXGBDHF-BFUOFWGJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.02α = 90
b = 67.33β = 98.58
c = 80.9γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bayer CropScienceGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description