5T6Q

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

Summary for 5T6Q

• Entry DOI: 10.2210/pdb5t6q/pdb
• Descriptor: Cytochrome P450 4B1, PROTOPORPHYRIN IX CONTAINING FE, N-OCTANE, ... (4 entities in total)
• Functional Keywords: cytochrome p450, fatty acid omega-hydroxylase, cyp4b1, octane, oxidoreductase
• Biological source: Oryctolagus cuniculus (Rabbit)
• Total number of polymer chains: 1
• Total formula weight: 58578.10

Authors

Hsu, M.,Johnson, E.F. (deposition date: 2016-09-01, release date: 2017-02-15, Last modification date: 2024-10-23)

Primary citation

Hsu, M.H.,Baer, B.R.,Rettie, A.E.,Johnson, E.F.
The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monooxygenase Complexed with Octane Discloses Several Structural Adaptations for omega-Hydroxylation.
J. Biol. Chem., 292:5610-5621, 2017

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 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.

PubMed: 28167536
DOI: 10.1074/jbc.M117.775494

Experimental method

X-RAY DIFFRACTION (2.701 Å)