Crystal Structure of Mycobacterium tuberculosis Polyketide Synthase 11 (PKS11) Reveals Intermediates in the Synthesis of Methyl-branched Alkylpyrones

Abstract

Background: Polyketide synthases (PKSs) synthesize complex lipid components of the cell wall in M. tuberculosis. Results: We determined the crystal structure of M. tuberculosis PKS11 and identified its substrate, intermediates, and product. Conclusion: M. tuberculosis PKS11 synthesizes a unique cyclic methyl-branched alkylpyrone. Significance: Our identification of alkylpyrones as the product of this PKS suggests a previously unknown component of the mycobacterial cell wall.

Exploiting the Biosynthetic Potential of Type III Polyketide Synthases

“…This is analogous to PKSA and PpASCL, whereby a replacement of bulky Thr197 in alfalfa CHS with a smaller Gly205 in PKSA and Gly225 in PpASCL is believed to widen the entrance of the acyl-binding tunnel, enabling them to utilize larger acyl-CoAs as starters [63]. The crystal structure of PKS11 was recently solved (PDB ID: 4JAP), and a buried hydrophobic tunnel was also revealed, together with a CoA-binding tunnel [73]. Co-crystallizations and in vitro enzyme assays revealed that PKS11 can catalyze the decarboxylative condensation of methylmalonyl-CoA with palmitoyl-CoA (C16) or stearoyl-CoA (C18), followed by another decarboxylative condensation of malonyl-CoA and lactonization to generate methylated alkylpyrones.…”

“…The ability of PKS11 to select different extenders at different stages of polyketide elongation is intriguing, and more structural studies in this aspect will be useful for the generation of clinically important unnatural polyketides. The crystal structure of PKS11 was recently solved (PDB ID: 4JAP), and a buried hydrophobic tunnel was also revealed, together with a CoA-binding tunnel [73]. Co-crystallizations and in vitro enzyme assays revealed that PKS11 can catalyze the decarboxylative condensation of methylmalonyl-CoA with palmitoyl-CoA (C16) or stearoyl-CoA (C18), followed by another decarboxylative condensation of malonyl-CoA and lactonization to generate methylated alkylpyrones.…”

“…Crystallographic analyses of the plant type III PKSs (alfalfa CHS [23], Scots pine STS [26], daisy 2-PS [35], rhubarb BAS [45], O. sativa CUS [49], C. microcarpa ACS and QNS [59], and brown alga phloroglucinol synthase [60]), the bacterial PKSs (S. coelicolor THNS [66], M. tuberculosis PKS11 [73] and PKS18 [72], A. vinelandii ArsC [80]), and of the fungal ORAS from N. crassa [83] have enabled the understanding of the basis of starter molecule selectivity, chain elongation, and cyclization of the linear polyketide intermediate. These structural studies have provided insights into the mechanistic details of type III PKSs, illustrating how subtle modifications in the active site cavity can expand the biosynthetic repertoire and result in the generation of diverse products.…”

Architecture of the polyketide synthase module: surprises from electron cryo-microscopy

“…Two recent KS crystal structures provide the first views of bona fide substrates as covalent intermediates in the KS active site. One structure is for a PKS that acts on acyl-CoA substrates [54], and the other is excised from a trans -AT pathway [51]. The spacious KS active sites appear to provide binding pockets adapted to their substrates, and based on these high-resolution substrate complexes, it is challenging to predict the position of a new building block delivered through the entrance for the module ACP.…”

Assessing the progress of Mycobacterium tuberculosis H37Rv structural genomics

“…M. smegmatis, a fast-growing saprophytic relative of Mtb, is a potential expression host for Mtb genes overcoming many of the restrictions of E. coli (36)(37)(38)(39). Unexpectedly, however, only nine proteins of H37Rv represented by 27 structures were produced in M. smegmatis (37,(40)(41)(42)(43)(44)(45)(46). Clearly the faster growth and production rates of E. coli ensure that it remains the most popular expression host.…”