Structures of a lipin/Pah phosphatidic acid phosphatase in distinct catalytic states reveal a signature motif for substrate recognition

Vitkovska, T.; Welcome, F. S.; Khayyo, V. I.; Gao, S.; Wymore, T.; Airola, M. V.

doi:10.1101/2025.06.16.660012

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bioRxiv · 10.1101/2025.06.16.660012

Structures of a lipin/Pah phosphatidic acid phosphatase in distinct catalytic states reveal a signature motif for substrate recognition

Vitkovska, T.·Welcome, F. S.·Khayyo, V. I.·Gao, S.·Wymore, T.·Airola, M. V.

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Abstract

Lipin/Pah phosphatidic acid phosphatases (PAPs) are Mg2+-dependent enzymes that catalyze the dephosphorylation of phosphatidic acid (PA) to produce diacylglycerol. Deficiency of lipin PAP activity in humans results in inflammatory disorders such as rhabdomyolysis and Majeed syndrome. Previously, we reported the first PAP enzyme structures of Tetrahymena thermophila (Tt) Pah2 at 3.0[A] resolution. Here, we present five new higher resolution (1.95-2.40[A]) structures of Tt Pah2, in distinct catalytic states, which represent active states of catalysis, including a phospho-Asp transition state mimic, and an inactive state with a distorted active site. The structures, in conjunction with flexible docking simulations and biochemical analysis, connect two highly conserved aspartate and arginine residues in magnesium coordination and recognition of the substrate PA. Overall, this provides a structural basis for catalysis and defines a signature Asp-Arg motif in lipin/Pah PAPs that enables recognition of their lipid substrate PA, providing insight into how the HAD domain of lipin/Pah PAPs evolved to act on a membrane embedded substrate.

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Vitkovska, T., Welcome, F. S., Khayyo, V. I., Gao, S., Wymore, T., Airola, M. V.. 2025-06-20. Structures of a lipin/Pah phosphatidic acid phosphatase in distinct catalytic states reveal a signature motif for substrate recognition. https://doi.org/10.1101/2025.06.16.660012

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