3TK3

Cytochrome P450 2B4 mutant L437A in complex with 4-(4-chlorophenyl)imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8001 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Investigation by site-directed mutagenesis of the role of cytochrome P450 2B4 non-active-site residues in protein-ligand interactions based on crystal structures of the ligand-bound enzyme.

Wilderman, P.R.Gay, S.C.Jang, H.H.Zhang, Q.Stout, C.D.Halpert, J.R.

(2012) Febs J. 279: 1607-1620

  • DOI: 10.1111/j.1742-4658.2011.08411.x

  • PubMed Abstract: 
  • Residues located outside the active site of cytochromes P450 2B have exhibited importance in ligand binding, structural stability and drug metabolism. However, contributions of non-active-site residues to the plasticity of these enzymes are not known ...

    Residues located outside the active site of cytochromes P450 2B have exhibited importance in ligand binding, structural stability and drug metabolism. However, contributions of non-active-site residues to the plasticity of these enzymes are not known. Thus, a systematic investigation was undertaken of unique residue-residue interactions found in crystal structures of P450 2B4 in complex with 4-(4-chlorophenyl)imidazole (4-CPI), a closed conformation, or in complex with bifonazole, an expanded conformation. Nineteen mutants distributed over 11 sites were constructed, expressed in Escherichia coli and purified. Most mutants showed significantly decreased expression, especially in the case of interactions found in the 4-CPI structure. Six mutants (H172A, H172F, H172Q, L437A, E474D and E474Q) were chosen for detailed functional analysis. Among these, the K(s) of H172F for bifonazole was ∼ 20 times higher than for wild-type 2B4, and the K(s) of L437A for 4-CPI was ∼ 50 times higher than for wild-type, leading to significantly altered inhibitor selectivity. Enzyme function was tested with the substrates 7-ethoxy-4-(trifluoromethyl)coumarin, 7-methoxy-4-(trifluoromethyl)coumarin and 7-benzyloxyresorufin (7-BR). H172F was inactive with all three substrates, and L437A did not turn over 7-BR. Furthermore, H172A, H172Q, E474D and E474Q showed large changes in k(cat)/K(M) for each of the three substrates, in some cases up to 50-fold. Concurrent molecular dynamics simulations yielded distances between some of the residues in these putative interaction pairs that are not consistent with contact. The results indicate that small changes in the protein scaffold lead to large differences in solution behavior and enzyme function.


    Related Citations: 
    • Structures of cytochrome P450 2B4 complexed with the antiplatelet drugs ticlopidine and clopidogrel .
      Gay, S.C.,Roberts, A.G.,Maekawa, K.,Talakad, J.C.,Hong, W.X.,Zhang, Q.,Stout, C.D.,Halpert, J.R.
      (2010) Biochemistry 49: 8709
    • Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4.
      Zhao, Y.,Sun, L.,Muralidhara, B.K.,Kumar, S.,White, M.A.,Stout, C.D.,Halpert, J.R.
      (2007) Biochemistry 46: 11559
    • 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.,Stout, C.D.,Halpert, J.R.
      (2004) J.Biol.Chem. 279: 27294
    • Plasticity of cytochrome P450 2B4 as investigated by hydrogen-deuterium exchange mass spectrometry and X-ray crystallography.
      Wilderman, P.R.,Shah, M.B.,Liu, T.,Li, S.,Hsu, S.,Roberts, A.G.,Goodlett, D.R.,Zhang, Q.,Woods, V.L.,Stout, C.D.,Halpert, J.R.
      (2010) J.Biol.Chem. 285: 38602
    • 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
    • Structural Analysis of Mammalian Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator tert-Butylphenylacetylene: Insight into Partial Enzymatic Activity
      C Gay, S.,Zhang, H.,Wilderman, P.R.,Roberts, A.G.,Liu, T.,Li, S.,Lin, H.L.,Woods Jr., V.L.,Stout, C.D.,Hollenberg, P.F.,Halpert, J.R.
      (2011) Biochemistry 50: 4903
    • 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
    • Crystal structures of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole: ligand-induced structural response through alpha-helical repositioning.
      Gay, S.C.,Sun, L.,Maekawa, K.,Halpert, J.R.,Stout, C.D.
      (2009) Biochemistry 48: 4762


    Organizational Affiliation

    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA. pwilderman@ucsd.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2B4
A, B, C, D
476Oryctolagus cuniculusGene 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, B, C, D
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, B, C, D
4-(4-CHLOROPHENYL)IMIDAZOLE
C9 H7 Cl N2
DVKIFCXVRCGAEE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8001 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 232.910α = 90.00
b = 232.910β = 90.00
c = 56.960γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SSRLdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2012-05-02
    Type: Database references