PPM1B utilizes a trinuclear metal architecture for phosphatase activity

Stevens, R. P.; Solodushko, V.; Wierzbicki, A.; Rich, T. C.; Alexeyev, M. F.; Thompson, M. K.; Stone, M.; Hall, C.; deWeever, A.; Sayner, S. L.; Stevens, T.; Andrews, J.; Prakash, A.; Honkanen, R. E.; Lee, J. Y.; Salter, E. A.; Swingle, M. R.

doi:10.64898/2026.04.23.720145

bioRxiv · 10.64898/2026.04.23.720145

PPM1B utilizes a trinuclear metal architecture for phosphatase activity

Stevens, R. P.·Solodushko, V.·Wierzbicki, A.·Rich, T. C.·Alexeyev, M. F.·Thompson, M. K.·Stone, M.·Hall, C.·deWeever, A.·Sayner, S. L.·Stevens, T.·Andrews, J.·Prakash, A.·Honkanen, R. E.·Lee, J. Y.·Salter, E. A.·Swingle, M. R.

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Abstract

The metal-dependent protein phosphatase (PPM/PP2C) family regulates innate immune and cell death pathways through reversible phosphorylation. Although these enzymes contain a conserved third Mg2+/Mn2+ ion (M3) that is essential for activity, its chemical role in phosphate hydrolysis has remained unclear. Here, we report studies that reveal PPM1B promotes cell death during Pseudomonas aeruginosa infection and utilizes a trinuclear metal center in which M3 directly coordinates the substrate phosphate, positioning it for in-line SN2 hydrolysis. In addition to substrate orientation, M3 positions a water molecule to protonate the departing alkoxide, stabilizing the leaving-group. Functionally, M3 substitutes for the arginine clamp in phosphoprotein phosphatases (PPP), revealing that these evolutionarily distinct phosphatase families have converged on the same chemical strategy through fundamentally different catalytic architectures. Together, these findings define a three-metal mechanism in PPM phosphatases and identify the M3 site as a rare and potentially druggable feature for immune and infectious diseases.

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Stevens, R. P., Solodushko, V., Wierzbicki, A., Rich, T. C., Alexeyev, M. F., Thompson, M. K., Stone, M., Hall, C., deWeever, A., Sayner, S. L., Stevens, T., Andrews, J., Prakash, A., Honkanen, R. E., Lee, J. Y., Salter, E. A., Swingle, M. R.. 2026-04-27. PPM1B utilizes a trinuclear metal architecture for phosphatase activity. https://doi.org/10.64898/2026.04.23.720145

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