4UYM

Crystal structure of sterol 14-alpha demethylase (CYP51B) from a pathogenic filamentous fungus Aspergillus fumigatus in complex with voriconazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Functional Characterization of Cytochrome P450 Sterol Alpha-Demethylase (Cyp51B) from Aspergillus Fumigatus and Molecular Basis for the Development of Antifungal Drugs

Hargrove, T.Y.Warwzak, Z.Lamb, D.C.Guengerich, F.P.Lepesheva, G.I.

(2015) J.Biol.Chem. 290: 23916

  • DOI: 10.1074/jbc.M115.677310
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aspergillus fumigatus is the opportunistic fungal pathogen that predominantly affects the immunocompromised population and causes 600,000 deaths/year. The cytochrome P450 51 (CYP51) inhibitor voriconazole is currently the drug of choice, yet the trea ...

    Aspergillus fumigatus is the opportunistic fungal pathogen that predominantly affects the immunocompromised population and causes 600,000 deaths/year. The cytochrome P450 51 (CYP51) inhibitor voriconazole is currently the drug of choice, yet the treatment efficiency remains low, calling for rational development of more efficient agents. A. fumigatus has two CYP51 genes, CYP51A and CYP51B, which share 59% amino acid sequence identity. CYP51B is expressed constitutively, whereas gene CYP51A is reported to be inducible. We expressed, purified, and characterized A. fumigatus CYP51B, including determination of its substrate preferences, catalytic parameters, inhibition, and x-ray structure in complexes with voriconazole and the experimental inhibitor (R)-N-(1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide (VNI). The enzyme demethylated its natural substrate eburicol and the plant CYP51 substrate obtusifoliol at steady-state rates of 17 and 16 min(-1), respectively, but did not metabolize lanosterol, and the topical antifungal drug miconazole was the strongest inhibitor that we identified. The x-ray crystal structures displayed high overall similarity of A. fumigatus CYP51B to CYP51 orthologs from other biological kingdoms but revealed phylum-specific differences relevant to enzyme catalysis and inhibition. The complex with voriconazole provides an explanation for the potency of this relatively small molecule, whereas the complex with VNI outlines a direction for further enhancement of the efficiency of this new inhibitory scaffold to treat humans afflicted with filamentous fungal infections.


    Organizational Affiliation

    Swansea University, Swansea, Wales SA2 8PP, United Kingdom, and.,From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.,From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, the Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232 galina.i.lepesheva@vanderbilt.edu.,the Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-ALPHA STEROL DEMETHYLASE
A, B
470Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)Mutation(s): 2 
EC: 1.14.13.-
Find proteins for E9QY26 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
Go to UniProtKB:  E9QY26
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
A, B
Voriconazole
(2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoropyrimidin-4-yl)-1-(1H-1,2,4-triazol-1-yl)butan-2-ol
C16 H14 F3 N5 O
BCEHBSKCWLPMDN-MGPLVRAMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VORKd: 423 - 429 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 109.193α = 90.00
b = 109.193β = 90.00
c = 90.211γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references
  • Version 1.2: 2015-10-07
    Type: Database references