Effects of the E310A Mutation of Cytochrome P450 4B1 (CYP4B1) on n-Octane binding and Heme Ruffling

Experimental Data Snapshot

  • Resolution: 2.67 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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Noncovalent interactions dominate dynamic heme distortion in cytochrome P450 4B1.

Jennings, G.K.Hsu, M.H.Shock, L.S.Johnson, E.F.Hackett, J.C.

(2018) J Biol Chem 293: 11433-11446

  • DOI: https://doi.org/10.1074/jbc.RA118.004044
  • Primary Citation of Related Structures:  
    6C93, 6C94

  • PubMed Abstract: 

    Cytochrome P450 4B1 (4B1) functions in both xenobiotic and endobiotic metabolism. An ester linkage between Glu-310 in 4B1 and the 5-methyl group of heme facilitates preferential hydroxylation of terminal (ω) methyl groups of hydrocarbons (HCs) and fatty acids compared with ω-1 sites bearing weaker C-H bonds. This preference is retained albeit diminished 4-fold for the E310A mutant, but the reason for this is unclear. Here, a crystal structure of the E310A-octane complex disclosed that noncovalent interactions maintain heme deformation in the absence of the ester linkage. Consistent with the lower symmetry of the heme, resonance Raman (RR) spectroscopy revealed large enhancements of RR peaks for high-spin HC complexes of 4B1 and the E310A mutant relative to P450 3A4. Whereas these enhancements were diminished in RR spectra of a low-spin 4B1- N -hydroxy- N '-(4-butyl-2-methylphenyl)formamidine complex, a crystal structure indicated that this inhibitor does not alter heme ruffling. RR spectra of Fe 2+ -CO HC complexes revealed larger effects of HC length in E310A than in 4B1, suggesting that reduced rigidity probably underlies increased E310A-catalyzed (ω-1)-hydroxylation. Diminished effects of the HC on the position of the Fe-CO stretching mode in 4B1 suggested that the ester linkage limits substrate access to the CO. Heme ruffling probably facilitates autocatalytic ester formation by reducing inhibitory coordination of Glu-310 with the heme iron. This also positions the 5-methyl for a reaction with the proposed glutamyl radical intermediate and potentially enhances oxo-ferryl intermediate reactivity for generation of the glutamyl radical to initiate ester bond formation and ω-hydroxylation.

  • Organizational Affiliation

    Massey Cancer Center and Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 4B1497Oryctolagus cuniculusMutation(s): 1 
Gene Names: CYP4B1
Find proteins for P15128 (Oryctolagus cuniculus)
Explore P15128 
Go to UniProtKB:  P15128
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15128
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C34 H32 Fe N4 O4
Query on OCT

Download Ideal Coordinates CCD File 
C [auth A]N-OCTANE
C8 H18
Experimental Data & Validation

Experimental Data

  • Resolution: 2.67 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.435α = 90
b = 109.435β = 90
c = 126.443γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM031001

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description