3R1B

Open crystal structure of cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Analysis of Mammalian Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator tert-Butylphenylacetylene: Insight into Partial Enzymatic Activity.

Gay, S.C.Zhang, H.Wilderman, P.R.Roberts, A.G.Liu, T.Li, S.Lin, H.L.Zhang, Q.Woods, V.L.Stout, C.D.Hollenberg, P.F.Halpert, J.R.

(2011) Biochemistry 50: 4903-4911

  • DOI: 10.1021/bi200482g
  • Primary Citation of Related Structures:  3R1A
  • Also Cited By: 3TK3, 3UAS

  • PubMed Abstract: 
  • A combined structural and computational analysis of rabbit cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene (tBPA) has yielded insight into how the enzyme retains partial activity. Since conjugation to ...

    A combined structural and computational analysis of rabbit cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene (tBPA) has yielded insight into how the enzyme retains partial activity. Since conjugation to tBPA modifies a highly conserved active site residue, the residual activity of tBPA-labeled 2B4 observed in previous studies was puzzling. Here we describe the first crystal structures of a modified mammalian P450, which show an oxygenated metabolite of tBPA conjugated to Thr 302 of helix I. These results are consistent with previous studies that identified Thr 302 as the site of conjugation. In each structure, the core of 2B4 remains unchanged, but the arrangement of plastic regions differs. This results in one structure that is compact and closed. In this conformation, tBPA points toward helix B', making a 31° angle with the heme plane. This conformation is in agreement with previously performed in silico experiments. However, dimerization of 2B4 in the other structure, which is caused by movement of the B/C loop and helices F through G, alters the position of tBPA. In this case, tBPA lies almost parallel to the heme plane due to the presence of helix F' of the opposite monomer entering the active site to stabilize the dimer. However, docking experiments using this open form show that tBPA is able to rotate upward to give testosterone and 7-ethoxy-4-trifluoromethylcoumarin access to the heme, which could explain the previously observed partial activity.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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

    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA. scgay@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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
A, B, C, D
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
TB2
Query on TB2

Download SDF File 
Download CCD File 
A, B, C, D
(4-tert-butylphenyl)acetaldehyde
C12 H16 O
VMLYBYNXKMHLIJ-UHFFFAOYSA-N
 Ligand Interaction
CM5
Query on CM5

Download SDF File 
Download CCD File 
A, B, D
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
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 193.924α = 90.00
b = 153.691β = 122.22
c = 129.665γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SSRLdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance