Structure of cytochrome P450 PimD suggests epoxidation of the polyene macrolide pimaricin occurs via a hydroperoxoferric intermediate

Abstract

We present the X-ray structure of PimD, both substrate-free and in complex with 4,5-desepoxypimaricin. PimD is a cytochrome P450 monooxygenase with native epoxidase activity that is critical in the biosynthesis of the polyene macrolide antibiotic pimaricin. Intervention in this secondary metabolic pathway could advance the development of drugs with improved pharmacologic properties. Epoxidation by P450 typically includes formation of a charge-transfer complex between an oxoferryl pi-cation radical species (Compound I) and the olefin pi-bond as the initial intermediate. Catalytic and structural evidence presented here suggest that epoxidation of 4,5-desepoxypimaricin proceeds via a hydroperoxoferric intermediate (Compound 0). The oxygen atom of Compound 0 distal to the heme iron may insert into the double bond of the substrate to make an epoxide ring. Stereoelectronic features of the putative transition state suggest substrate-assisted proton delivery.

Figure 1

Chemical structures of the polyene macrolide antibiotics.

Figure 2. Overall structure of PimD

A and B, Superimposed structures of substrate-free (wheat) and 4,5-desepoxypimaricin-bound (light blue) PimD are shown with the α-helices labeled. The protein backbone is depicted by ribbon and the heme (orange) and 4,5-desepoxypimaricin by spheres. Desepoxypimaricin is colored according the elements with the carbon atoms yellow, oxygen red and nitrogen blue. A, Distal protein surface with respect to heme. B, Image is rotated ~ 90° toward viewer. C, Stereoscopic view of PimD with 4,5-desepoxypimaricin bound in the active site. For clarity, only a few residues (green) within 6 Å from 4,5-desepoxypimaricin are shown. Fragments of the protein backbone are shown as gray ribbon. Color schemes for 4,5-desepoxypimaricine and heme are as in A and B. Loops are labeled with the numbers for a range of the amino acid residues constituting the loop. 2Fo-Fc electron density map (blue wire mesh) is calculated with the 4,5-desepoxypimaricin coordinates omitted from the input. Images are generated using PYMOL (DeLano, 2002).

Figure 3. Sequence alignments between polyene macrolide monooxygenases

Multiple sequence alignments between PimD (Streptomyces natalensis), NysL (Streptomyces noursei) and AmphL (Streptomyces nodosus) are shown. Accession numbers of the proteins in the Swiss-Prot/TrEMBL (http://us.expasy.org/sprot) database are given next to the name of the protein. Alignments were performed using CLUSTALW program online (Thompson et al., 1994). The figure was generated using ESPript (Gouet et al., 1999). The secondary structure annotation and residue numbering at the top correspond to PimD. Amino acid residues within 6 Å from the substrate in the active site are labeled with blue (clustered) and green (isolated) triangles. Iron proximal cystein ligand is marked with a red star. Grey stars highlight residues in alternate conformations. If aligned pair-wise, PimD is 57% identical to NysL, and 55% identical to AmphL. NysL and AmphL share 71% sequence identity and are more closely related.

Figure 4. 4,5-desepoxypimaricin interactions in the catalytic site

A, The H-bonding interactions of 4,5-desepoxypimaricin are indicated by the dashed lines with the distances in Angstroms. The I-helix is traced by a grey ribbon. A fragment of the 2Fo-Fc electron density map (blue mesh) indicates rotation of the Ser238 side chain in toward the I-helix grove and H-bonding to the carbonyl oxygen of A234. Color schemes for the heme (van der Waals spheres) and 4,5-desepoxypimaricin (sticks) are as in Fig. 2 with the H atoms at the C4-C5 double bond shown in grey. B, UV-vis absorbance spectra are shown for PimD (5 μM) in the ferric low-spin state (red), ferrous CO-bound form (blue), and ferric substrate-bound form at 100 μM 4,5-desepoxypimaricin (green). The latter trace represents a mix between the low-spin and high-spin forms. All spectra were recorded at room temperature in 100 mM potassium phosphate, pH 7.5, and 10% glycerol.

Figure 5. Structure-based mechanism of epoxidation

Three different views of the disposition of atoms in the O₂-scission site are shown in A, B and C to emphasize orientation of the to-be-epoxidized double bond C4-C5 and position of W2168 (red sphere) with respect to each other and the heme iron. A clipped fragment of 4,5-desepoxypimaricin accommodating the reaction site is shown in yellow with oxygen atoms in red and hydrogen atoms in grey. Ala234 is shown with carbon atoms in grey. Blue arrow points are collinear with the C4-C5 π-orbitals. Fragment of the I-helix is shown as a grey ribbon. Distances are in Angstroms. In red are the distances between W2168 and the C4 or C5 carbons. D, Epoxidation reaction scheme. Substrate atoms are outlined in grey.

Figure 6. PimD-catalyzed epoxidation via peroxide shunt pathway

A, High-pressure liquid chromatography traces at 304 nm corresponding to reactions of PimD (10 μM) with 4,5-desepoxypimaricin (100 μM) in the presence of 10 mM ascorbic acid driven by either H₂O₂ (100 mM), peracetic acid (2 mM) or iodosobenzene (1 mM). Mix of the authentic 4,5-desepoxypimaricin (S) and pimaricin (P) was used as a standard. A new peak is only observed in the presence of H₂O₂ that corresponds to the epoxidation of the substrate to pimaricin. B, protection effect of 10 mM ascorbic acid (filled bars) on the overall recovery of the substrate 4,5-desepoxypimaricin (left panel) and the product pimaricin (right panel) from the oxidative damage by free-radicals generated upon PimD reaction with H₂O₂. Empty bars represent recovery of the substrate and product in absence of ascorbic acid.

Figure 7. Stopped-flow analysis of PimD interactions with iodosobenzene and peroxynitrite

A, Rapid-scan absorbance spectra for the first 45 s of reaction between PimD (5 μM) and iodosobenzene (150 μM) selected in 3 s intervals are shown. Inset: kinetics recorded at 435 and 380 nm. B, singular value decomposition analysis of data in A using A→ B → C → D kinetic model, with k₁ = 0.271 s⁻¹, k₂ = 1.141 s⁻¹, and k₃ = 0.0581 s⁻¹. Inset: time dependence of the different forms of PimD in the reaction with iodosobenzene. C, rapid-scan absorbance spectra for the first 45 s of reaction between PimD (5 μM) and peroxyntrite (250 μM) selected in 3 s intervals are shown. Inset: kinetics recorded at 433 nm. All data were collected at 10°C in 100 mM potassium phosphate, pH 7.4.