Structural rearrangements of a polyketide synthase module during its catalytic cycle

Area of Science:

• Biochemistry
• Structural Biology
• Natural Product Synthesis

Background:

• Polyketide synthases (PKS) are large enzyme complexes responsible for producing a vast array of bioactive natural products.
• These natural products are crucial scaffolds for many pharmaceuticals.
• PKS enzymes feature a modular architecture, with each module catalyzing specific modifications.

Purpose of the Study:

• To elucidate the structural dynamics of a full-length PKS module during its catalytic cycle.
• To understand the role of the acyl carrier protein (ACP) domain in substrate transfer and processing.
• To provide insights into the conformational changes of catalytic domains, particularly the ketoreductase (KRED).

Main Methods:

• Determined three-dimensional structures of a pikromycin PKS module using electron cryo-microscopy (cryo-EM).
• Confirmed biochemical states via liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS).
• Analyzed the positioning and dynamics of the ACP domain and catalytic domains throughout the enzymatic cycle.

Main Results:

• Captured distinct structural snapshots of the PKS module at key stages: substrate loading, beta-keto intermediate formation, and beta-hydroxy product generation.
• Demonstrated precise positioning of the ACP domain for sequential interactions with ketosynthase (KS), acyltransferase (AT), and ketoreductase (KRED) domains.
• Observed significant conformational rearrangements in the KRED domain, optimizing it for reduction of the ACP-bound intermediate.

Conclusions:

• The study reveals the dynamic mechanism of substrate processing and transfer within a PKS module.
• Structural insights into ACP and catalytic domain movements are critical for understanding PKS function.
• Findings facilitate the rational design of novel PKS modules and engineered pathways for pharmaceutical development.