Polyketides biosynthesis, reaction mechanism

Nature gives us some illustrative examples of iterative methodologies in its biochemical mechanisms. The fatty acid-polyketide biosynthesis is one of them. The assembly of acyl units by sequential Claisen-type condensations to form a polyketide or fatty acid takes place at a multi-enzyme complex, at which the initial molecule is lengthened by one C2-unit per pass of a reaction cycle (Fig. 2). 

Fig. 4 (a) Structures of aromatic polyketides produced by A. arborescens. (b) Proposed enzyme reaction mechanism of PCS, (c) OKS, and (d) PKS3. A hypothetical scheme for the involvement of OKS and as yet unidentified ketoreductase in the biosynthesis of anthrones and anthraquinones is also included... 

Gatto et al m characterized the mechanism of L-pipecolic acid formation by cyclodeaminase RapL from L-lysine within rapamycin biosynthesis, which is a hybrid NRP—polyketide antibiotic (Figure 25(a)). RapL was characterized by biochemical assays to require cofactor nicotinamide adenine dinucleotide (NAD+) and an oxidative cyclodeamination reaction mechanism corresponding to ornithine cyclodeamination was proposed based on ESI-FTMS analysis of RapL reaction products (Figure 25(b)). 

P. A. Frey and A. D. Hegeman, Enzymatic Reaction Mechanisms, Oxford University Press, Oxford, 2007. A more basic treatment is in two Oxford Primers by J. Mann, Chemical Aspects of Biosynthesis, OUP, 1994 and by T. Bugg, Introduction to Enzyme and Coenzyme Chemistry, OUP, Oxford, 2004. A more comprehensive treatment is in J. E. McMurry and T. P. Begley, The Organic Chemistry of Biological Pathways, Roberts, 2005. For an introduction to biosynthesis, see F. J. keeper and J. C. Vederas, Biosynthesis Polyketides and Vitamins, Springer, 2000. 

Methyl transfer reactions play a significant part in the modifications of aromatic polyketides, both of the polyketide core [61,62] as well as of several of the sugar moieties [44,53]. In Streptomyces, more than 20 amino acid sequences have been found that may represent enzymes involved in methyl transfer reactions in the biosynthesis of aromatic polyketides [149]. One of these enzymes, the S-adenosyl-L-methionine-dependent DnrK, is involved in the methylation of the C-4 hydroxyl group in daunorubicin/doxorubicin biosynthesis (Scheme 10, step 12). The subunit of the homo-dimeric enzyme displays a fold typical for small-molecule methyltransferases. The structure of the ternary complex with bound products S-adenosyl-L-homocysteine and 4-methoxy-8-rhodomycin provided insights into the structural basis of substrate recognition and catalysis [149]. The position and orientation of the substrates suggest an Sn2 mechanism for methyl transfer, and mutagenesis experiments show that there is no catalytic base in the vicinity of the substrate. Rate enhancement is thus most likely due to orientational and proximity effects [149]. 

Mechanistic studies are an important tool to understand how the biosynthesis of natural products occurs in nature and how to mimic their synthesis in the laboratory. Progress in this field includes the biomimetric synthesis of flavonolignan diastereomers in milk thistle (13JOC7594) and the chemoenzymatic synthesis of tetrahydropyran-containing polyketides (13AGE13215). In the synthetic domain, DFT calculations and experimental assays have been carried out to explain the multiple mechanisms involved in the palladium(II)-catalyzed Sn2 reactions of aUylic alcohols to prepare chiral tetrahydropyran derivatives (13JOC7664). 

As briefly explained in Sect. 1.2.1, the -270 residue TE domain catalyses either a hydrolysis or an intermolecular cyclisation reaction to terminate the biosynthesis of polyketides and fatty acids, releasing the final prodnct from the assembly line. The TE domain exhibits an a/fi-hydrolase fold and is dimeric in modular type I PKS systems. The mechanism of both hydrolytic cleavage and macrolactonisa-tion commences with the transfer of the polyketide chain from the final ACP onto the active site serine of the TE, forming an acyl-TE intermediate. The hydrolytic... 

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