1SUO

Structure of mammalian cytochrome P450 2B4 with bound 4-(4-chlorophenyl)imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9 {angstrom} resolution: Insight into the range of P450 conformations and coordination of redox partner binding.

Scott, E.E.White, M.A.He, Y.A.Johnson, E.F.Stout, C.D.Halpert, J.R.

(2004) J.Biol.Chem. 279: 27294-27301

  • DOI: 10.1074/jbc.M403349200
  • Also Cited By: 3UAS, 3TK3, 3R1B, 3R1A, 3ME6, 3KW4, 2BDM

  • PubMed Abstract: 
  • A 1.9-A molecular structure of the microsomal cytochrome P450 2B4 with the specific inhibitor 4-(4-chlorophenyl)imidazole (CPI) in the active site was determined by x-ray crystallography. In contrast to the previous experimentally determined 2B4 stru ...

    A 1.9-A molecular structure of the microsomal cytochrome P450 2B4 with the specific inhibitor 4-(4-chlorophenyl)imidazole (CPI) in the active site was determined by x-ray crystallography. In contrast to the previous experimentally determined 2B4 structure, this complex adopted a closed conformation similar to that observed for the mammalian 2C enzymes. The differences between the open and closed structures of 2B4 were primarily limited to the lid domain of helices F through G, helices B' and C, the N terminus of helix I, and the beta(4) region. These large-scale conformational changes were generally due to the relocation of conserved structural elements toward each other with remarkably little remodeling at the secondary structure level. For example, the F' and G' helices were maintained with a sharp turn between them but are placed to form the exterior ceiling of the active site in the CPI complex. CPI was closely surrounded by residues from substrate recognition sites 1, 4, 5, and 6 to form a small, isolated hydrophobic cavity. The switch from open to closed conformation dramatically relocated helix C to a more proximal position. As a result, heme binding interactions were altered, and the putative NADPH-cytochrome P450 reductase binding site was reformed. This suggests a structural mechanism whereby ligand-induced conformational changes may coordinate catalytic activity. Comparison of the 2B4/CPI complex with the open 2B4 structure yields insights into the dynamics involved in substrate access, tight inhibitor binding, and coordination of substrate and redox partner binding.


    Related Citations: 
    • A Truncation of 2B Subfamily Cytochromes P450 Yields Increased Expression Levels, Increased Solubility, and Decreased Aggregation While Retaining Function
      Scott, E.E.,Spatzenegger, M.,Halpert, J.R.
      (2001) Arch.Biochem.Biophys. 395: 57
    • An Open Conformation of Mammalian Cytochrome P450 2B4 at 1.6 A 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


    Organizational Affiliation

    Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston 77555-1031, USA. eescott@ku.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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
CPZ
Query on CPZ

Download SDF File 
Download CCD File 
A
4-(4-CHLOROPHENYL)IMIDAZOLE
C9 H7 Cl N2
DVKIFCXVRCGAEE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CPZIC50: 40 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.215 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 233.386α = 90.00
b = 233.386β = 90.00
c = 56.380γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
MOSFLMdata reduction
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance