Multifunctional P450 Monooxygenase CftA Diversifies the Clifednamide Pool through Tandem C–H Bond Activations

Abstract

Polycyclic tetramate macrolactams (PTMs) are a class of structurally complex hybrid polyketide-nonribosomal peptide (PK-NRP) natural products produced by diverse bacteria. Several PTMs display pharmaceutically interesting bioactivities, and the early stages of PTM biosynthesis involving polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymology are well studied. However, the timing and mechanisms of post PKS-NRPS oxidations by P450 monooxygenases encoded in PTM biosynthetic gene clusters (BGCs) remain poorly characterized. Here we demonstrate that CftA, encoded in clifednamide-type PTM BGCs, is a multifunctional P450 monooxygenase capable of converting the C29–C30 ethyl side chain of ikarugamycin to either a C29–C30 methyl ketone or a C29–C30 hydroxymethyl ketone through C–H bond activation, resulting in the formation of clifednamide A or clifednamide C, respectively. We also report the complete structure of clifednamide C solved via multidimensional NMR (COSY, HSQC, HMBC, NOESY, and TOCSY) using material purified from an engineered Streptomyces strain optimized for production. Finally, the in vitro reconstitution of recombinant CftA catalytic activity revealed the oxidation cascade for sequential conversion of ikarugamycin to clifednamide A and clifednamide C. Our findings confirm prior genetics-based predictions on the origins of clifednamide complexity via P450s encoded in PTM BGCs and place CftA into a growing group of multifunctional P450s that tailor PTM natural products through late-stage regioselective C–H bond activation.

Discovery of Oxidized Polycyclic Tetramate Macrolactams Bearing One or Two Rings through Combinatorial Pathway Reassembly

“…To date, all known PoTeM-associated CYPs are found to modify the polyketide moiety of PoTeMs, ,,,, and the 3-hydroxylation of the ornithine residue was exclusively catalyzed by C-3 hydroxylase, which belongs to the fatty acid desaturase family. , To provide direct evidence for the function of SahD and SahE, the corresponding genes were expressed in E. coli , and the purified enzymes were tested for activity with putative substrates. Since the native redox system required for the activity of SahD and SahE was unknown, the heterologous redox partners ferredoxin-NADP + reductase ( sel FdR0978) and ferredoxin ( sel Fdx1499) from Synechococcus elongates were used for the activity assay .…”

A Mechanistic Understanding of the Distinct Regio‐ and Chemoselectivity of Multifunctional P450s by Structural Comparison of IkaD and CftA Complexed with Common Substrates

“…The 5/5‐type pactamide C ( 6 ) was recognized by both IkaD and CftA as a substrate, and was mainly converted to pactamide M ( 6 a ), a C10 hydroxylated product (Figures 4C, S12, S20; Tables S9–S10). Pactamide M ( 6 a ) only displayed different stereochemistry on the 5/5 ring compared to combamide G, a product generated in vivo by Mg1D (a homolog of IkaD and CftA) [14b] . In addition to 6 a , both IkaD and CftA also produced the C10 and C29 dihydroxylated product 6 b , the structure of which was proposed based on that combamide G was reported to be converted in vivo to combamide B (with both C10 and C29 hydroxyl groups) by Mg1D.…”

“…For example, the P450 IkaD from Streptomyces xiamenensis 318 catalyzes the epoxidation of the C7=C8 double bond in ikarugamycin ( 1 ) to afford epoxyikarugamycin ( 1 a ), and a subsequent C29 hydroxylation, leading to capsimycin G ( 1 b ); [14e] in contrast, CftA from Streptomyces sp.JV178 (sharing ≈53 % sequence identity with IkaD) also uses 1 as the native substrate, and catalyzes a four‐electron oxidation at C29 of 1 to yield C29‐ketonyl in clifednamide A ( 1 c ), followed by a weak C30 hydroxylation to produce clifednamide C ( 1 d ) (Figure 1A). [15] Unlike other multifunctional P450s that are reported to be restricted to a single substrate, [16] in vivo combinatorial biosynthetic studies suggest that both IkaD and CftA display relaxed substrate flexibility to recognize multiple PoTeM substrates with different carbocycle ring systems [14b,17] (Figure 1B). Therefore, it provides a unique opportunity to study IkaD and CftA as models for interrogating the structure‐function relationship of multifunctional P450s, since they share the same substrate for multiple oxidations but display distinct oxidation patterns.…”

Electrochemical transformations catalyzed by cytochrome P450s and peroxidases

“…, transforming poorly reactive linear or cyclic alkanes to alcohols and alkenes to epoxides. 267–273 Fig. 10 summarizes bioelectrochemical transformations catalyzed by Cyt P450s, including heteroatom oxygenation, C-hydroxylation, S-oxidation, N-hydroxylation, epoxide formation and heteroatom dealkylation.…”