Human cytochrome P450 1A1 structure and utility in understanding drug and xenobiotic metabolism

Abstract

Cytochrome P450 (CYP) 1A1 is an extrahepatic monooxygenase involved in the metabolism of endogenous substrates and drugs, as well as the activation of certain toxins and environmental pollutants. CYP1A1 is particularly well known for its ability to biotransform polycyclic aromatic hydrocarbons, such as benzo[a]pyrene in tobacco smoke, into carcinogens. CYP1A1 possesses functional similarities and differences with human CYP1A2 and CYP1B1 enzymes, but the structural basis for this has been unclear. We determined a 2.6 Å structure of human CYP1A1 with the inhibitor α-naphthoflavone. α-Naphthoflavone binds within an enclosed active site, with the planar benzochromen-4-one core packed flat against the I helix that composes one wall of the active site, and the 2-phenyl substituent oriented toward the catalytic heme iron. Comparisons with previously determined structures of the related cytochrome P450 1A2 and 1B1 enzymes reveal distinct features among the active sites that may underlie the functional variability of these enzymes. Finally, docking studies probed the ability of CYP1A structures to assist in understanding their known in vitro interactions with several typical substrates and inhibitors.

Keywords: Cytochrome P450; Cytochrome P450 1A1; Docking; Drug Metabolism; Membrane Proteins; X-ray Crystallography; Xenobiotics.

FIGURE 1.

Overall structures. A, human CYP1A1 colored from blue at the N terminus to red at the C terminus with heme as gray sticks and ANF as pink sticks. Inset, ANF structure and numbering. B, comparison between CYP1A1 (blue), CYP1A2 (yellow), and CYP1B1 (green) aligned by Cα atoms.

FIGURE 2.

Comparison of the break in the F helix. A, CYP1A1. B, CYP1A2. C, CYP1B1. ANF ligand is shown as gray sticks.

FIGURE 3.

CYP1A1/ANF active site colored as in Fig. 1A showing 2|F_o| − |F_c| electron density map contoured at 1 σ (blue mesh) for ANF. A, view face on. B, view edge on. Structural elements surrounding ANF include the I helix (yellow), the F and G helices (green), the B′ region (blue), the K/β_1–4 loop (orange), and the residues that normally comprise the β₄ loop (red).

FIGURE 4.

CYP1A1 (colored as in Fig. 1A) hydrogen bonding (dashed lines) networks around ANF. A, interactions between residues in the E and F helices (green), I helix (yellow), and the β4 loop (red). B, interactions between the B′/C region (blue) and I helix residues (yellow).

FIGURE 5.

Wall eye stereo comparisons between the active site residues. A, CYP1A1 (blue) versus CYP1A2 (yellow). B, CYP1A1 (blue) versus CYP1B1 (green). Residue numbering is CYP1A1/CYP1A2 and CYP1A1/CYP1B1, respectively. Heme is shown as dark gray sticks with a rust sphere for iron.

FIGURE 6.

Comparisons between the active site cavity topologies. A and B, front view (A) and side view (B) of CYP1A1 (blue) and CYP1A2 (yellow) cavities. C and D, front view (C) and side view (D) of CYP1A1 (blue) and CYP1B1 (green) cavities.

FIGURE 7.

Ligands docked into CYP1A1 and CYP1A2 x-ray structures. A, CYP1A1/ANF experimental structure (blue) and CYP1A1 with ANF docked lowest energy pose (gray). B, CYP1A2/ANF experimental structure (yellow) and CYP1A2 with ANF docked lowest energy pose (gray). C, CYP1A1 (blue) with lowest energy pose of phenacetin (black). D, CYP1A2 (yellow) with lowest energy pose of phenacetin (black). E, CYP1A1 (blue) with lowest energy poses of methoxyresorufin (black) and ethoxyresorufin (gray). F, CYP1A2 (yellow) with lowest energy poses of methoxyresorufin (black) and ethoxyresorufin (gray). G, CYP1A1 (blue) with representative poses for B(a)P (black and gray). H, CYP1A1 (blue) with representative poses for resveratrol (black and gray). I, structures of ligands docked into CYP1A enzymes and sites of metabolism (arrows).