2BDM

Structure of Cytochrome P450 2B4 with Bound Bifonazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.

Zhao, Y.White, M.A.Muralidhara, B.K.Sun, L.Halpert, J.R.Stout, C.D.

(2006) J.Biol.Chem. 281: 5973-5981

  • DOI: 10.1074/jbc.M511464200
  • Also Cited By: 3UAS, 3TK3, 3R1B, 3R1A, 3ME6, 3KW4

  • PubMed Abstract: 
  • To better understand ligand-induced structural transitions in cytochrome P450 2B4, protein-ligand interactions were investigated using a bulky inhibitor. Bifonazole, a broad spectrum antifungal agent, inhibits monooxygenase activity and induces a typ ...

    To better understand ligand-induced structural transitions in cytochrome P450 2B4, protein-ligand interactions were investigated using a bulky inhibitor. Bifonazole, a broad spectrum antifungal agent, inhibits monooxygenase activity and induces a type II binding spectrum in 2B4dH(H226Y), a modified enzyme previously crystallized in the presence of 4-(4-chlorophenyl)imidazole (CPI). Isothermal titration calorimetry and tryptophan fluorescence quenching indicate no significant burial of protein apolar surface nor altered accessibility of Trp-121 upon bifonazole binding, in contrast to recent results with CPI. A 2.3 A crystal structure of 2B4-bifonazole reveals a novel open conformation with ligand bound in the active site, which is significantly different from either the U-shaped cleft of ligand-free 2B4 or the small active site pocket of 2B4-CPI. The O-shaped active site cleft of 2B4-bifonazole is widely open in the middle but narrow at the top. A bifonazole molecule occupies the bottom of the active site cleft, where helix I is bent approximately 15 degrees to accommodate the bulky ligand. The structure also defines unanticipated interactions between helix C residues and bifonazole, suggesting an important role of helix C in azole recognition by mammalian P450s. Comparison of the ligand-free 2B4 structure, the 2B4-CPI structure, and the 2B4-bifonazole structure identifies structurally plastic regions that undergo correlated conformational changes in response to ligand binding. The most plastic regions are putative membrane-binding motifs involved in substrate access or substrate binding. The results allow us to model the membrane-associated state of P450 and provide insight into how lipophilic substrates access the buried active site.


    Related Citations: 
    • An open conformation of mammalian cytochrome P450 2B4 at 1.6-resolution
      Scott, E.E.,He, Y.A.,Wester, M.R.,White, M.A.,Chin, C.C.,Halpert, J.R.,Johnson, E.F.,Stout, C.D.
      (2003) Proc.Natl.Acad.Sci.USA 100: 13196
    • Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding
      Scott, E.E.,White, M.A.,He, Y.A.,Johnson, E.F.,D Stout, C.,Halpert, J.R.
      (2004) J.Biol.Chem. 279: 27294


    Organizational Affiliation

    Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA. yozhao@utmb.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2B4
A
476Oryctolagus cuniculusMutation(s): 9 
Gene Names: CYP2B4
EC: 1.14.14.1
Find proteins for P00178 (Oryctolagus cuniculus)
Go to UniProtKB:  P00178
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CM5
Query on CM5

Download SDF File 
Download CCD File 
A
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE; CYMAL-5
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-N
 Ligand Interaction
TMI
Query on TMI

Download SDF File 
Download CCD File 
A
1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE
BIFONAZOLE
C22 H18 N2
OCAPBUJLXMYKEJ-QFIPXVFZSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TMIIC50: 900 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 203.210α = 90.00
b = 203.210β = 90.00
c = 103.450γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALAdata scaling
CCP4data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description