Phosphatase Subfamily PPM1A

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Phosphatase Classification: Fold PPM (PP2C): Superfamily PPM (PP2C): Family PPM (PP2C): Subfamily PPM1A

Evolution

The PPM1A subfamily is found across opisthokonts. Budding yeast PTC2, PTC3 and PTC4 are inferred to be PPM1As, because they have the same substrate with holozoa PPM1A, human CDK2/yeast Cdc28.

Human has three members: PPM1A, PPM1B and PPM1N. PPM1A and PPM1B arose by gene duplication in jawed vertebrates, but not through whole-genome duplication, as they do not locate in the same double-conserved synteny (see Genomicus). Human PPM1N probably emerged in placentals and was lost by independent evolutionary events in different lineages, as implied by internal orthology database and BLAST NR database. For BLAST, human PPM1N was defined as the hits that have a better (lower) E-values than human PPM1A and PPM1B. Thus, all three human members, as well as other jawed vertebrate PPM1As, originated from a single ancestral gene. The PPM1A subfamily is also found in monosiga. Thus, the subfamily is most likely to emerge in holozoa.

Domains

The PPM1A subfamily has the phosphatase domain and a signature C-terminal domain next to catalytic domain, PP2C_C in Pfam. The PP2C_C domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the phosphatase domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain. The PP2C_C domain is only present in PPM1A subfamily, and may be absent from Monosiga and yeast homologs, which have no sequence similarity in this region (and PTC4 has no sequence after the phosphatase domain). Human PPM1A and PPM1N have a predicted nuclear localization signal (NLS) at N-terminal. PPM1As from other organisms have weak NLS by prediction.

Functions

PPM1A regulates different signaling pathways, such as MAPK, SAPK/JNK, NF-kappaB, TGF-beta pathways.

Common substrates of human PPM1A and PPM1B
  • IKKβ at Ser-177 and Ser-181. Both human PPM1A and PPM1B dephosphorylated IKKβ at Ser-177 and Ser-181 and termination of IKKβ-induced NF-κB activation [1, 2].
  • CDK9 at Thr-186 in the T-loop. Both PPM1A and PPM1B dephosphorylated CDK9 at Thr-186 in the T-loop [3]. CDK9 is the catalytic subunit of a general RNA polymerase II elongation factor known as positive transcription elongation factor b (P-TEFb). The kinase function of P-TEFb requires phosphorylation of Thr-186 in the T-loop of Cdk9 to allow substrates to access the catalytic core of the enzyme [3].
  • Moesin at Thr-588. Both PPM1A and PPM1B dephosphorylated the membrane-F-actin linking protein moesin at Thr-588, which is phosphorylated during activation of platelets [4].
  • CDK2 at Thr-160 [5]. Yeast PPM1As, PTC2 and PTC3 (but not PTC4), can dephosphorylate Cdc28, the ortholog of human CDK2, at the same site (Thr-169) [6].
Different functions of PPM1A and PPM1B
PPM1A (PP2Cα)

Human PPM1A is widely expressed across different tissues, according to RNA-seq data from GTEx. Below are the substrates reported for PPM1A but not PPM1B, but we cannot rule out PPM1B may dephosphorylate some of them:

  • mGluR3 at Ser-845. mGluR3 is a metabotropic glutamate receptor 3. It interacted with PPM1A through a C-terminal region from 836 to 855. The region was specific for mGluR3 and was not found in mGluR2, which was its cloest gene in sequence. The region contained Ser-845 phosphorylated by PKA. As PPM1A dephosphorylated the region in vitro, it was probably dephosphorylated Ser-845 [7].
  • RelA at Ser-536 and Ser-276. PPM1A directly dephosphorylated RelA at the two positions and selectively inhibited NF-kappaB pathway [8].
  • p85 subunit of PI3K at Ser-608 [9].
  • p38. PPM1A directly interacted with and dephosphorylated MAPK p38, classfied as CMGC:MAPK:p38 in Kinbase [10].
  • MKK6. PPM1A dephosphorylated MAPKK MKK6, classified as STE:STE7:MEK3 in KinBase [10].
  • SEK1. PPM1A dephosphorylated MAPKK SEK1, classified as STE:STE7:MEK4 in KinBase [10].
  • Axin. PPM1A formed a complex with Dvl, beta-catenin, and Axin. It dephosphorylated Axin, a negative regulator of WNT signaling, both in vitro and in vivo. The dephosphorylation resulted in decreasing Axin's half-life. PPM1A therefore is a positive regulator of WNT signal [11].
  • PKCdelta. In addition to PPM1A, PP1 and PP2A (PP3) can also dephosphorylate PKCdelta, albeit lower specific activity [12].
  • SMAD1 and SMAD2/3 at SxS motif [13, 14]. SMADs are critical players in TGF-beta signaling. The dephosphorylation increases their nuclear exporter activity. (Be careful: the Cell paper was flagged; the other paper is of the same author.)
  • RanBP3, nuclear exporter. PPM1A directly interacted with and dephosphorylated RanBP3 at Ser-58 both in vitro and in vivo. The dephosphorylation promoted RanBP3's ability to export Smad2/3 and terminate TGF-beta signaling [15].

In addition, PPM1A regulated cell cycle [16].

PPM1B (PP2Cβ)

PPM1B is expressed in a broad types of tissues, most abundantly in skeletal muscle as shown by RNA-seq data from GTEx and northern blot [17]. Below are the substrates reported for PPM1A but not PPM1B, though PPM1B may dephosphorylate some of them:

  • TAK1 at Ser-192. PPM1B but not PPM1A associated with and dephosphorylated TAK1 in vitro [18]. TAK1 is a player in SAPK/JNK pathway, upstream of MKK4/MKK6 and JNK. It belongs to TKL group, MLK family and TAK1 subfamily according the KinBase classification. It emerged in holozoa. In the same study, it was shown that PPM1B did not dephosphorylate MKK6 and did not associate with MEKK3, MKK4, MKK6, JNK, or p38, which was dephosphorylated and inactivated by PPM1A [18]. TAK1 can be also dephosphorylated by another PPM, PPM1L.
  • TBK1 at Ser-172. TBK1 is a kinase activates antiviral response. The dephosphorylation therefore results in negatively regulates antiviral response [19].
  • PAX2 [20]. PAX2 is a transcription factor which is activated by the phosphorylation at Ser/Thr sites within its C-terminal activation domain, depending on WNT signals and JNK activity.
  • PPARγ (peroxisome-proliferator-activated receptor γ) at Ser-112 [21]. PPARγis a nuclear receptor whose activity is altered by the phosphorylation state of Ser-112 and Ser-273. PPM1B can directly dephosphorylate PPARγ both in intact cells and in vitro. In addition, PPM1B specifically targeted Ser-112 rather than Ser-273, which increase PPARγ activity [21]..

PPM1B interacts with the proteins, but there is no direct evidence that they are the substrates:

  • Erythroid Kruppel-like factor, a erythroid-specific transcription factor. Mouse Ppm1b probably has an indirect role in regulating EKLF turnover via its zinc finger domain [22].

PPM1B is phosphorylated by PKA at Ser-195 [23]. The Ser-195 is a signature of PPM1A subfamily, because 1) all PPM1A members have serine at the position, 2) PPMs of other subfamilies only have serine, occasionally.

PPM1B is modified with ISG15 at least through Lys-12 and Lys-142 [24]. ISG15 is an interferon-upregulated ubiquitin-like protein, which is covalently conjugated to various cellular proteins (ISGylation). ISG15 is found mainly in marsupials and placentals. In comparison, Lys-12 is found in all vertebrate PPM1Bs and PPM1As. Lys-142 is only found in primate and eutheria PPM1Bs, and was replaced by Thr in rodent PPM1B, by Asp or Glu even Ser in marsupial, reptile and fish PPM1Bs, by Gln and Ser even His in PPM1A.

Human PPM1N

PPM1N's function is unknown. It is generally expressed at low level across tissues except spleen (see RNA-seq data from GTEx).

Fruit fly alph: negatively regulates RAS/MAPK and SAPK/JNK

Alphabet, the PPM1A in fruit fly, negatively regulates RAS/MAPK signaling in Drosophila [25] and stress-activated protein kinase (SAPK) [26]. However, its substrates in these signaling pathways are unclear.

Budding yeast PTC2, PTC3 and PTC4

The three yeast PPM1As, PTC2, PTC3 and PTC4 are reviewed in table 1 in [27] and in [28]. PTC2 and PTC3 (but not PTC4) can dephosphorylate Cdc28 at Thr-169 [6]. All three phosphatases are involved in high osmolarity glycerol (HOG) pathway, particularly PTC2 and PTC3 can directly dephosphorylate the p38 kinase, Hog1 [29]. PTC2 can also dephosphorylate Ire1 to downregulate endoplasmic reticulum (ER) unfolded protein response [30].

References

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  2. Sun W, Yu Y, Dotti G, Shen T, Tan X, Savoldo B, Pass AK, Chu M, Zhang D, Lu X, Fu S, Lin X, and Yang J. PPM1A and PPM1B act as IKKbeta phosphatases to terminate TNFalpha-induced IKKbeta-NF-kappaB activation. Cell Signal. 2009 Jan;21(1):95-102. DOI:10.1016/j.cellsig.2008.09.012 | PubMed ID:18930133 | HubMed [Sun09]
  3. Wang Y, Dow EC, Liang YY, Ramakrishnan R, Liu H, Sung TL, Lin X, and Rice AP. Phosphatase PPM1A regulates phosphorylation of Thr-186 in the Cdk9 T-loop. J Biol Chem. 2008 Nov 28;283(48):33578-84. DOI:10.1074/jbc.M807495200 | PubMed ID:18829461 | HubMed [Wang08]
  4. Hishiya A, Ohnishi M, Tamura S, and Nakamura F. Protein phosphatase 2C inactivates F-actin binding of human platelet moesin. J Biol Chem. 1999 Sep 17;274(38):26705-12. DOI:10.1074/jbc.274.38.26705 | PubMed ID:10480873 | HubMed [Hishiya99]
  5. Cheng A, Kaldis P, and Solomon MJ. Dephosphorylation of human cyclin-dependent kinases by protein phosphatase type 2C alpha and beta 2 isoforms. J Biol Chem. 2000 Nov 3;275(44):34744-9. DOI:10.1074/jbc.M006210200 | PubMed ID:10934208 | HubMed [Cheng00]
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  11. Strovel ET, Wu D, and Sussman DJ. Protein phosphatase 2Calpha dephosphorylates axin and activates LEF-1-dependent transcription. J Biol Chem. 2000 Jan 28;275(4):2399-403. DOI:10.1074/jbc.275.4.2399 | PubMed ID:10644691 | HubMed [Strovel00]
  12. Srivastava J, Goris J, Dilworth SM, and Parker PJ. Dephosphorylation of PKCdelta by protein phosphatase 2Ac and its inhibition by nucleotides. FEBS Lett. 2002 Apr 10;516(1-3):265-9. DOI:10.1016/s0014-5793(02)02500-0 | PubMed ID:11959144 | HubMed [Srivastava02]
  13. Lin X, Duan X, Liang YY, Su Y, Wrighton KH, Long J, Hu M, Davis CM, Wang J, Brunicardi FC, Shi Y, Chen YG, Meng A, and Feng XH. PPM1A functions as a Smad phosphatase to terminate TGFbeta signaling. Cell. 2006 Jun 2;125(5):915-28. DOI:10.1016/j.cell.2006.03.044 | PubMed ID:16751101 | HubMed [Lin06]
  14. Duan X, Liang YY, Feng XH, and Lin X. Protein serine/threonine phosphatase PPM1A dephosphorylates Smad1 in the bone morphogenetic protein signaling pathway. J Biol Chem. 2006 Dec 1;281(48):36526-32. DOI:10.1074/jbc.M605169200 | PubMed ID:16931515 | HubMed [Duan06]
  15. Dai F, Shen T, Li Z, Lin X, and Feng XH. PPM1A dephosphorylates RanBP3 to enable efficient nuclear export of Smad2 and Smad3. EMBO Rep. 2011 Oct 28;12(11):1175-81. DOI:10.1038/embor.2011.174 | PubMed ID:21960005 | HubMed [Dai11]
  16. Ofek P, Ben-Meir D, Kariv-Inbal Z, Oren M, and Lavi S. Cell cycle regulation and p53 activation by protein phosphatase 2C alpha. J Biol Chem. 2003 Apr 18;278(16):14299-305. DOI:10.1074/jbc.M211699200 | PubMed ID:12514180 | HubMed [Ofek03]
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