Rational Engineering of Phospholipase D Unlocks Robust Catalysis for Phosphatidylserine Formation

Phosphatidylserine (PS), a major brain phospholipid, supports the central nervous system’s health and may alleviate cognitive decline, including in Alzheimer’s disease. A key challenge in green enzymatic PS synthesis is the suppression of hydrolysis while enhancing PLD-catalyzed transphosphatidylation. Here, we developed a mechanism-guided engineering strategy for Streptomyces antibioticus phospholipase D (SaPLD). The substitution of W187I increased the PS yield to 58.3%, while V380W improved thermostability. Combining beneficial mutations generated SaPLD-R7 (W187I/V380W/G381A), which overcame the activity–stability trade-off and achieved up to 95.8% PS yield using the enzyme produced by 5 L scale fermentation. Molecular dynamics simulations showed that SaPLD-R7 enhanced substrate binding and catalysis by shortening the key active site distances and reducing local flexibility. Solvent contact and energy analyses further indicated improved stability. This work establishes a structure–mechanism–function framework for enhancing PLD transphosphatidylation and provides a robust enzymatic route for high-efficiency PS production as a valuable functional food ingredient.