Structural rearrangements of a polyketide synthase module during its catalytic cycle

• Published in: Nature (London) Vol. 510; no. 7506; pp. 560 - 564
• Main Authors: Whicher, Jonathan R., Dutta, Somnath, Hansen, Douglas A., Hale, Wendi A., Chemler, Joseph A., Dosey, Annie M., Narayan, Alison R. H., Håkansson, Kristina, Sherman, David H., Smith, Janet L., Skiniotis, Georgios
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 26.06.2014; Nature Publishing Group
• Subjects: 101/28; 101/58; 631/535/1258/1259; 82; 82/83; Acyl Carrier Protein - chemistry; Acyl Carrier Protein - metabolism; Acyl Carrier Protein - ultrastructure; Acyltransferases - chemistry; Acyltransferases - metabolism; Acyltransferases - ultrastructure; Alcohol Oxidoreductases - chemistry; Alcohol Oxidoreductases - metabolism; Alcohol Oxidoreductases - ultrastructure; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Bacterial Proteins - ultrastructure; Biocatalysis; Biosynthesis; Catalytic Domain; Chromatography; Cryoelectron Microscopy; Crystal structure; Fourier transforms; Health aspects; Humanities and Social Sciences; letter; Liquid chromatography; Macrolides - metabolism; Mass spectrometry; Models, Molecular; multidisciplinary; Observations; Polyketide Synthases - chemistry; Polyketide Synthases - metabolism; Polyketide Synthases - ultrastructure; Polyketides; Protein Structure, Tertiary; Protein-protein interactions; Proteins; Science; Streptomyces; Streptomyces - enzymology
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/nature13409

Polyketide synthases (PKSs) are multidomain enzymes that produce polyketides, which form the basis of many therapeutic agents; here, electron cryo-microscopy is used to probe the structure of an intact module of a multi-enzyme PKS in different functional states. Modular polyketide synthase structure Polyketide synthases (PKSs) are multi-domain enzyme complexes producing polyketides, a large class of secondary metabolites — in other words, natural products. Two papers from Georgios Skiniotis and colleagues use cryo-electron microscopy to probe the structure of an intact module of a full-length multienzyme PKS module involved in pikromycin biosynthesis in the bacterium Streptomyces venezuelae in different functional states. The structures reveal how the ketosynthase, acyltransferase, ketoreductase and acyl carrier protein (ACP) domains interact during the catalytic cycle. In each state the ACP is differentially positioned to facilitate intermediate transfer for the next catalytic step and for transfer to the next module. The polyketide synthase (PKS) mega-enzyme assembly line uses a modular architecture to synthesize diverse and bioactive natural products that often constitute the core structures or complete chemical entities for many clinically approved therapeutic agents 1 . The architecture of a full-length PKS module from the pikromycin pathway of Streptomyces venezuelae creates a reaction chamber for the intramodule acyl carrier protein (ACP) domain that carries building blocks and intermediates between acyltransferase, ketosynthase and ketoreductase active sites (see accompanying paper 2 ). Here we determine electron cryo-microscopy structures of a full-length pikromycin PKS module in three key biochemical states of its catalytic cycle. Each biochemical state was confirmed by bottom-up liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry. The ACP domain is differentially and precisely positioned after polyketide chain substrate loading on the active site of the ketosynthase, after extension to the β-keto intermediate, and after β-hydroxy product generation. The structures reveal the ACP dynamics for sequential interactions with catalytic domains within the reaction chamber, and for transferring the elongated and processed polyketide substrate to the next module in the PKS pathway. During the enzymatic cycle the ketoreductase domain undergoes dramatic conformational rearrangements that enable optimal positioning for reductive processing of the ACP-bound polyketide chain elongation intermediate. These findings have crucial implications for the design of functional PKS modules, and for the engineering of pathways to generate pharmacologically relevant molecules.