Protein Ser/Thr phosphatases compose a PPP family that includes type-2 PP2A, PP4, and PP6, each with essential functions. The human PP6 gene rescues sit4 ts mutants of Saccharomyces cerevisiae, and Sit4 phosphatase function depends on multiple Sit4-associated protein (SAP) subunits. We report here finding a SAPS sequence domain encoded in only a single gene each in Schizosaccharomyces pombe, Caenorhabditis elegans, and Drosophila but in three distinct open reading frames in Xenopus, Mus musculus, and Homo sapiens. The SAPS proteins are more divergent in sequence than PP6. Northern hybridization showed differential distribution of the human SAPS-related mRNA in multiple human tissues, named as PP6R1, PP6R2, and PP6R3. Antibodies were generated, distribution of endogenous PP6, PP6R1, PP6R2, and PP6R3 proteins was examined by immunoblotting, and the abundance of mRNA and protein in various tissues did not match. FLAG-tagged PP6R1 and PP6R2 expressed in HEK293 cells co-precipitated endogenous PP6, but not PP2A or PP4, showing specificity for recognition of phosphatases. The SAPS domain of PP6R1 alone was sufficient for association with PP6, and this predicts that conserved sequence motifs in the SAPS domain accounts for the specificity. FLAG-PP6R1 and FLAG-PP6R2 co-precipitated HA-IB⑀. Knockdown of PP6 or PP6R1 but not PP6R3 with siRNA significantly enhanced degradation of endogenous IB⑀ in response to tumor necrosis factor-␣. The results show SAPS domain subunits recruit substrates such as IB⑀ as one way to determine specific functions for PP6.Protein phosphorylation by kinases and protein dephosphorylation by phosphatases is the most common mechanism for regulating cellular processes. Protein phosphatases fall into major families based on different structures, specificity and catalytic mechanisms. The protein Ser/Thr phosphatase PPP family comprises the type-1 and type-2A phosphatases that are conserved throughout eukaryotic evolution. The PP2A, 2 PP4, and PP6 phosphatases are sensitive to inhibition by low doses of okadaic acid that distinguishes them from the type-1 phosphatase. The regulation and function of PP2A has been studied the most (1, 2), and there are a few reports about PP4 (3), but the function of PP6 is essentially unknown in metazoans. In Saccharomyces cerevisiae genetic studies have implicated the essential Sit4 phosphatase, the homolog of PP6, in regulation of G 1 to S progression (4 -6). In addition, Sit4 affects a variety of processes including transcription, translation, bud formation, glycogen metabolism, monovalent ion homeostasis, H ϩ transport, and telomere function (7-11) (for reviews, see Refs. 12 and 13). Mammalian PP6 is a functional homolog of Sit4 because human PP6 can rescue a temperature-sensitive mutant of sit4 from arrest in G 1 phase of the cell cycle, a phenotype that is rescued neither by type-1 phosphatase nor PP2A (14, 15). Sit4 associates with the protein product of the essential S. cerevisiae gene Tap42, which acts as a multicopy suppressor of the sit4 temperature-sensitiv...

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Protein phosphatase 6 (PP6) is an essential Ser/Thr phosphatase conserved among eukaryotes. The Saccharomyces cerevisiae homologue of PP6 called Sit4 depends on association with SAPS domain subunits. This study used a human SAPS domain subunit FLAG-PP6R1 to identify endogenous interacting proteins. Mass spectrometry identified coprecipitating proteins as PP6 catalytic subunit and three ankyrin repeat proteins (Ankrd28, Ankrd44, and Ankrd52). These proteins have extensive sequence identity to one another but segregate into separate branches on a phylogenetic tree for vertebrate species, suggesting individual biological functions. Tagged Ankrd28 coprecipitated with PP6, not with PP2A or PP4, and with SAPS domain subunits PP6R1 and PP6R3. Tagged PP6 coprecipitated endogenous SAPS domain subunits and Ankrd28. The C-terminal region of PP6R1 was sufficient to coprecipitate Ankrd28, but not PP6, demonstrating that PP6R1 acts as a scaffold with separate regions for binding to PP6 and to Ankrd28. Endogenous PP6 holoenzymes with PP6R1 and PP6R3 subunits were resolved by DEAE chromatography and eluted together with Ankrd28 at Mr > 440 kDa from Superose 12. Knockdown of PP6R1 or Ankrd28, but not PP6R3, produced equivalent enhancement of IkappaBepsilon degradation in response to TNFalpha. The results suggest that PP6 functions as a heterotrimer, composed of the PP6 catalytic subunit bound to a SAPS domain scaffold subunit that associates with Ankrd28. We propose that the SAPS and ankyrin repeat regulatory subunits determine the function and specificity of PP6.

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