Cryo-EM and cellular dissection uncover versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Protein phosphatase 2A (PP2A) methylesterase 1 (PME-1) is cancer-promoting but essential for development, and long-believed to remove carboxymethylation, a central modification, from the common PP2A core enzyme but not diverse holoenzymes that target broad cellular signaling by recognizing specific disordered motifs via regulatory subunits. On the contrary, our biochemical dissection and high-resolution cryo-EM structural analysis of a PP2A-B’ holoenzyme-PME-1 complex reveal that PME-1 disordered motifs, including phosphatase substrate-mimicking motifs, tether to the holoenzyme at remote sites, block its substrate binding, and allow large structural shifts in both holoenzyme and PME-1 to enable multiptle dynamic structured contacts and induce methylesterase activation toward the holoenzyme. PME-1 inhibitor and B’-interface mutations differentially modulate cellular PP2A methylation and allow us to uncover cellular PME-1 functions in AKT-p53 signaling. Our studies demonstrate how dynamic structured cores and disordered motifs create versatile activities and lay a foundation for investigating and targeting multifaceted activities toward broad PP2A complexes in cellular signaling.

Identification of PP1–Gadd34 substrates involved in the unfolded protein response using K-BIPS, a method for phosphatase substrate identification

The K-BIPS method exploits the phosphatase sensitivity of kinase-catalyzed biotinylation to identify the substrates of phosphatases, including here the substrates of the PP1–Gadd34 complex.