Mammalian Microsomal Cytochrome P450 Monooxygenase Pamela A. Williams, Jose Cosme, Vandana Sridhar, Eric F. Johnson, Duncan E. McRee  Molecular Cell  Volume 5, Issue 1, Pages 121-131 (January 2000) DOI: 10.1016/S1097-2765(00)80408-6

Figure 1 Electron Density Map The final σA (Read 1986) weighted 2Fo − Fc electron density map contoured at 1 σ and superimposed on the final model. Helix I runs horizontally across the center of the picture. The potential interaction between the side chain of Thr-298 and the main chain carbonyl of Ala-294 can be seen just above the heme. Molecular Cell 2000 5, 121-131DOI: (10.1016/S1097-2765(00)80408-6)

Figure 2 The Topology of P450 2C5/3LVdH (A) The overall fold of P450 2C5/3LVdH is colored from blue at the N terminus to red at the C terminus. The general location of the F–G loop, omitted from the final model, is shown in magenta. The designations used for the elements of secondary structure are adopted from those used for the heme domain of P450 BM3 (Ravichandran et al. 1993). (B) The mutated residues that enabled the crystallization of P450 2C5 are close to a crystal contact formed by helix F and the N-terminal end of helix G in one molecule (yellow) with a symmetry-related molecule (cyan). The mutated residues are rendered in the lower molecule as CPK atoms and are found on the surface of helix F and in the portion of the F–G loop that has clear electron density. A samarium atom, shown in magenta, binds on the two-fold crystallographic axis where it interacts with charged side chains from the two molecules. This crystal contact limits the likely location of the portion of the F–G loop that could not be modeled. Molecular Cell 2000 5, 121-131DOI: (10.1016/S1097-2765(00)80408-6)

Figure 3 Conservation of the Heme Binding Site The heme is sandwiched between helix I on the distal side and helix L on the proximal side of the protein. The side chain Sχ of Cys-432 (data not shown) is an axial ligand to the heme iron and is found immediately upstream of helix L. These features are spatially conserved with other P450s as shown by the superposition of P450 BM3 (yellow) on the structure of 2C5/3LVdH (cyan). In addition, helix C is well conserved in space. The two molecules were superimposed by an rms fit of Cα atoms in helix L, the β bulge, and the central portion of helix I. The β strand 1–4 and the immediate upstream region located across the distal surface of the heme from the I helix exhibit extensive divergence, with an rms deviation of 3.3 Å between Cα atoms. Molecular Cell 2000 5, 121-131DOI: (10.1016/S1097-2765(00)80408-6)

Figure 4 Progesterone Docked in the Active Site of P450 2C5 Two views of the position and orientation of progesterone are shown together with elements of secondary structure (cyan) and amino acid side chains that form the substrate binding cavity. The atom types are colored as in Figure 3 with the carbon atoms of the side chains colored gray and progesterone shown in yellow. The C21 carbon of the docked progesterone is sufficiently close to the heme iron for hydroxylation to occur. (A) The view is looking across SRS-5, which includes L358, L359 and L363, toward SRS-4 in helix I, where D290, A294, and T298 reside. Three other SRS regions are depicted: SRS-1, the B–C loop containing L102, A113, and F114; SRS-2, helix F containing V205 and L208; and SRS-6, β2 containing F473 and V474. SRS-3 located on helix G is not in close proximity to the docked progesterone. Molecular Cell 2000 5, 121-131DOI: (10.1016/S1097-2765(00)80408-6)

Figure 5 A Comparison of the Topology of the Distal Surfaces of P450 2C5 and the Heme Domain of P450 BM3 Extensive structural divergence is seen in the positions of topological elements of P450 sC5 shown in cyan and P450 BM3 shown in yellow, particularly the N-terminal domain that includes helix A and the β sheet, β1. Significant differences are also evident in the positions of topological elements that form the substrate binding site. The largest differences occur for the B–C loop (SRS-1) and helix F (SRS-2). As a result, the overall shape of the substrate binding site in P450 2C5 is quite different from that of P450 BM3. The two molecules were superimposed as in Figure 3. Molecular Cell 2000 5, 121-131DOI: (10.1016/S1097-2765(00)80408-6)

Figure 6 Mechanism of Membrane Association (A) A ribbon diagram depicts the orientation of the distal surface shown in Figure 6B. The locations of epitopes recognized by antipeptide antibodies to family 2 P450s are mapped onto the structure (von Wachenfeldt and Johnson 1995). Epitopes that are masked by membrane binding are depicted in red, whereas epitopes that are exposed when the proteins are bound to membranes are shown in green. All of the epitopes that are masked in the membrane bound enzyme occur on one surface of the protein. (B) The surface of P450 2C5/3LVdH was rendered in INSIGHT II (MSI, San Diego) and colored according to hydophilicity (Engelman et al. 1986) as indicated on the color scale. The hydrophobic core of the membrane lies below the white line drawn, while the head groups are located above. The hydrophobic region (yellow and white) on the bottom of the molecule provides additional membrane interactions that contribute to the binding of 2C5/3LVdH to membranes and buries the epitopes shown in (A). In addition, this region contains the N terminus, which connects to the N-terminal transmembrane segment. Molecular Cell 2000 5, 121-131DOI: (10.1016/S1097-2765(00)80408-6)

Figure 7 Potential Site of NADPH Cytochrome P450 Reductase Interaction Two views of the proximal surface are shown in the same orientation as in Figure 6 with the monofacial membrane binding surface toward the bottom of the figure. (A) A ribbon diagram is shown with the residues where alanine substitutions disrupt interactions of P450 2B4 with CPR (Bridges et al. 1998) rendered as CPK atoms. Carbon atoms are depicted in green, sulfur atoms in yellow, nitrogen atoms in blue, and the heme is shown in red. (B) The electrostatic potential surface was calculated using DELPHI II (Honig and Nicholls 1995) with a probe radius of 1.4 Å and displayed using AVS (AVS Inc., Waltham, MA) with positive potential shown as blue and negative potential as red. The basic residues in P450 2C5, which are conserved in other microsomal P450s, form a positive electrostatic ring that is thought to steer the docking site near the heme to a negatively charged patch on CPR. Molecular Cell 2000 5, 121-131DOI: (10.1016/S1097-2765(00)80408-6)