3UAS

Cytochrome P450 2B4 covalently bound to the mechanism-based inactivator 9-ethynylphenanthrene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.939 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Potent Mechanism-Based Inactivation of Cytochrome P450 2B4 by 9-Ethynylphenanthrene: Implications for Allosteric Modulation of Cytochrome P450 Catalysis.

Zhang, H.Gay, S.C.Shah, M.Foroozesh, M.Liu, J.Osawa, Y.Zhang, Q.Stout, C.D.Halpert, J.R.Hollenberg, P.F.

(2013) Biochemistry 52: 355-364

  • DOI: 10.1021/bi301567z

  • PubMed Abstract: 
  • The mechanism-based inactivation of cytochrome P450 2B4 (CYP2B4) by 9-ethynylphenanthrene (9EP) has been investigated. The partition ratio and k(inact) are 0.2 and 0.25 min(-1), respectively. Intriguingly, the inactivation exhibits sigmoidal kinetics ...

    The mechanism-based inactivation of cytochrome P450 2B4 (CYP2B4) by 9-ethynylphenanthrene (9EP) has been investigated. The partition ratio and k(inact) are 0.2 and 0.25 min(-1), respectively. Intriguingly, the inactivation exhibits sigmoidal kinetics with a Hill coefficient of 2.5 and an S(50) of 4.5 μM indicative of homotropic cooperativity. Enzyme inactivation led to an increase in mass of the apo-CYP2B4 by 218 Da as determined by electrospray ionization liquid chromatography and mass spectrometry, consistent with covalent protein modification. The modified CYP2B4 was purified to homogeneity and its structure determined by X-ray crystallography. The structure showed that 9EP is covalently attached to Oγ of Thr 302 via an ester bond, which is consistent with the increased mass of the protein. The presence of the bulky phenanthrenyl ring resulted in inward rotations of Phe 297 and Phe 206, leading to a compact active site. Thus, binding of another molecule of 9EP in the active site is prohibited. However, results from the quenching of 9EP fluorescence by unmodified or 9EP-modified CYP2B4 revealed at least two binding sites with distinct affinities, with the low-affinity site being the catalytic site and the high-affinity site on the protein periphery. Computer-aided docking and molecular dynamics simulations with one or two ligands bound revealed that the high-affinity site is situated at the entrance of a substrate access channel surrounded by the F' helix, β1-β2 loop, and β4 loop and functions as an allosteric site to enhance the efficiency of activation of the acetylenic group of 9EP and subsequent covalent modification of Thr 302.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    Department of Pharmacology, The University of Michigan Medical School , Ann Arbor, Michigan 48109, USA.




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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0BV
Query on 0BV

Download SDF File 
Download CCD File 
A
phenanthren-9-ylacetaldehyde
9-ethylphenanthrene, oxidized and bound form
C16 H12 O
GLWZSGUBBSQBKG-UHFFFAOYSA-N
 Ligand Interaction
CM5
Query on CM5

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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
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
TAM
Query on TAM

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Download CCD File 
A
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.939 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.243 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.155α = 90.00
b = 90.155β = 90.00
c = 148.623γ = 120.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PDB_EXTRACTdata extraction
REFMACrefinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing
XPREPdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary