Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase

Elucidation of interface interactions between a dehydratase domain and an acyl carrier protein in cremimycin polyketide synthase

Modular polyketide synthases (PKSs) are multi-domain enzymes involved in the biosynthesis of polyketide natural products. The dehydratase (DH) domain catalyzes the dehydration of the β-hydroxyacyl unit attached to the acyl carrier protein (ACP) domain in modular PKS. Although the DH domain likely recognizes the cognate ACP domain during the dehydration reaction, the molecular basis of DH-ACP interactions remains elusive. In this study, we conducted cross-linking analysis using a pantetheine-type probe for investigating the ACP recognition of a fusion-DH protein generated from a split-DH domain of cremimycin PKS. Based on the AlphaFold 3-predicted model structure of the fusion-DH-ACP complex, DH-ACP interface residues were identified and validated by mutational analysis. Our findings provide the first detailed insights into domain-domain interactions between DH and ACP in modular PKSs.

The structure of full-length AFPK supports the ACP linker in a role that regulates iterative polyketide and fatty acid assembly

The polyketide synthases (PKSs) in microbes and the cytoplasmic fatty acid synthases in humans (FASs) are related enzymes that have been well studied. As a result, there is a paradigm explaining in general terms how FASs repeatedly use a set of enzymatic domains to produce simple fats, while PKSs use the domains in a much more complex manner to produce pharmaceuticals and other elaborate molecules. However, most animals also have PKSs that do not conform to the rules described in microbes, including a large family of enzymes that bridge fatty acid and polyketide metabolism, the animal FAS-like PKSs (AFPKs). Here, we present the cryoelectron microscopy structures of two AFPKs from sea slugs. While the AFPK resemble mammalian FASs, their chemical products mimic those of PKSs in complexity. How then does the architecture of AFPKs facilitate this structural complexity? Unexpectedly, chemical complexity is controlled not solely by the enzymatic domains but is aided by the dynamics of the acyl carrier protein (ACP), a shuttle that moves intermediates between these domains. We observed interactions between enzyme domains and the linker-ACP domain, which, when manipulated, altered the kinetic properties of the enzyme to change the resulting chemical products. This unveils elaborate mechanisms and enzyme motions underlying lipid and polyketide biochemistry across the domains of life.

Noncanonical Functions of Ketosynthase Domains in Type I Polyketide Synthases

Modular type I polyketide synthases (PKSs) are remarkable molecular machines that can synthesize structurally complex polyketide natural products with a wide range of biological activities. In these molecular machines, ketosynthase (KS) domains play a central role, typically by catalyzing decarboxylative Claisen condensation for polyketide chain extension. Noncanonical KS domains with catalytic functions rather than Claisen condensation have increasingly been evidenced, further demonstrating the capability of type I PKSs for structural diversity. This review provides an overview of the reactions involving unusual KS activities, including PKS priming, acyl transfer, Dieckmann condensation, Michael addition, aldol-lactonization bicyclization, C-N bond formation and decarbonylation. Insights into these reactions can deepen the understanding of PKS-based assembly line chemistry and guide the efforts for rational engineering of polyketide-related molecules.

Mutagenesis Supports AlphaFold Prediction of How Modular Polyketide Synthase Acyl Carrier Proteins Dock With Downstream Ketosynthases

The docking of an acyl carrier protein (ACP) domain with a downstream ketosynthase (KS) domain in each module of a polyketide synthase (PKS) helps ensure accurate biosynthesis. If the polyketide chain bound to the ACP has been properly modified by upstream processing enzymes and is compatible with gatekeeping residues in the KS tunnel, a transacylation reaction can transfer it from the 18.1-Å phosphopantetheinyl arm of the ACP to the reactive cysteine of the KS. AlphaFold-Multimer predicts a general interface for these transacylation checkpoints. Half of the solutions obtained for 50 ACP/KS pairs show the KS motif TxLGDP forming the first turn of an α-helix, as in reported structures, while half show it forming a type I β-turn not previously observed. Solutions with the latter conformation may represent how these domains are relatively positioned during the transacylation reaction, as the entrance to the KS active site is relatively open and the phosphopantetheinylated ACP serine and the reactive KS cysteine are relatively closer-17.2 versus 20.9 Å, on average. To probe the predicted interface, 20 mutations were made to KS surface residues within the model triketide lactone synthase P1-P6-P7. The activities of these mutants are consistent with the proposed interface.

Architecture of full-length type I modular polyketide synthases revealed by X-ray crystallography, cryo-electron microscopy, and AlphaFold2

Covering: up to the end of 2023Type I modular polyketide synthases construct polyketide natural products in an assembly line-like fashion, where the growing polyketide chain attached to an acyl carrier protein is passed from catalytic domain to catalytic domain. These enzymes have immense potential in drug development since they can be engineered to produce non-natural polyketides by strategically adding, exchanging, and deleting individual catalytic domains. In practice, however, this approach frequently results in complete failures or dramatically reduced product yields. A comprehensive understanding of modular polyketide synthase architecture is expected to resolve these issues. We summarize the three-dimensional structures and the proposed mechanisms of three full-length modular polyketide synthases, Lsd14, DEBS module 1, and PikAIII. We also describe the advantages and limitations of using X-ray crystallography, cryo-electron microscopy, and AlphaFold2 to study intact type I polyketide synthases.

How Acyl Carrier Proteins (ACPs) Direct Fatty Acid and Polyketide Biosynthesis

Megasynthases, such as type I fatty acid and polyketide synthases (FASs and PKSs), are multienzyme complexes responsible for producing primary metabolites and complex natural products. Fatty acids (FAs) and polyketides (PKs) are built by assembling and modifying small acyl moieties in a stepwise manner. A central aspect of FA and PK biosynthesis involves the shuttling of substrates between the domains of the multienzyme complex. This essential process is mediated by small acyl carrier proteins (ACPs). The ACPs must navigate to the different catalytic domains within the multienzyme complex in a particular order to guarantee the fidelity of the biosynthesis pathway. However, the precise mechanisms underlying ACP-mediated substrate shuttling, particularly the factors contributing to the programming of the ACP movement, still need to be fully understood. This Review illustrates the current understanding of substrate shuttling, including concepts of conformational and specificity control, and proposes a confined ACP movement within type I megasynthases.