5T6Q

Structure of cytochrome P450 4B1 (CYP4B1) complexed with octane: An n-Alkane and fatty acid omega-hydroxylase with a covalently bound heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monooxygenase Complexed with Octane Discloses Several Structural Adaptations for omega-Hydroxylation.

Hsu, M.H.Baer, B.R.Rettie, A.E.Johnson, E.F.

(2017) J. Biol. Chem. 292: 5610-5621

  • DOI: 10.1074/jbc.M117.775494

  • PubMed Abstract: 
  • P450 family 4 fatty acid ω-hydroxylases preferentially oxygenate primary C-H bonds over adjacent, energetically favored secondary C-H bonds, but the mechanism explaining this intriguing preference is unclear. To this end, the structure of rabbit P450 ...

    P450 family 4 fatty acid ω-hydroxylases preferentially oxygenate primary C-H bonds over adjacent, energetically favored secondary C-H bonds, but the mechanism explaining this intriguing preference is unclear. To this end, the structure of rabbit P450 4B1 complexed with its substrate octane was determined by X-ray crystallography to define features of the active site that contribute to a preference for ω-hydroxylation. The structure indicated that octane is bound in a narrow active-site cavity that limits access of the secondary C-H bond to the reactive intermediate. A highly conserved sequence motif on helix I contributes to positioning the terminal carbon of octane for ω-hydroxylation. Glu-310 of this motif auto-catalytically forms an ester bond with the heme 5-methyl, and the immobilized Glu-310 contributes to substrate positioning. The preference for ω-hydroxylation was decreased in an E310A mutant having a shorter side chain, but the overall rates of metabolism were retained. E310D and E310Q substitutions having longer side chains exhibit lower overall rates, likely due to higher conformational entropy for these residues, but they retained high preferences for octane ω-hydroxylation. Sequence comparisons indicated that active-site residues constraining octane for ω-hydroxylation are conserved in family 4 P450s. Moreover, the heme 7-propionate is positioned in the active site and provides additional restraints on substrate binding. In conclusion, P450 4B1 exhibits structural adaptations for ω-hydroxylation that include changes in the conformation of the heme and changes in a highly conserved helix I motif that is associated with selective oxygenation of unactivated primary C-H bonds.


    Organizational Affiliation

    the Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195.,From the Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037 and johnson@scripps.edu.,From the Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 4B1
A
497Oryctolagus cuniculusMutation(s): 0 
Gene Names: CYP4B1
EC: 1.14.14.1
Find proteins for P15128 (Oryctolagus cuniculus)
Go to Gene View: CYP4B1
Go to UniProtKB:  P15128
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OCT
Query on OCT

Download SDF File 
Download CCD File 
A
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.678α = 90.00
b = 109.678β = 90.00
c = 125.817γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-09-01 
  • Released Date: 2017-02-15 
  • Deposition Author(s): Hsu, M., Johnson, E.F.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM031001

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references
  • Version 1.2: 2017-04-12
    Type: Database references
  • Version 1.3: 2018-03-28
    Type: Author supporting evidence, Data collection