Last Updated: September 12, 2024
Phosphatases in Signal Transduction
Substantial evidence links both tyrosine and serine/threonine phosphorylation with increased cellular growth, proliferation and differentiation. Removal of the incorporated phosphates must be a necessary event in order to turn off the proliferative signals. This suggests that phosphatases may function as growth suppressors or tumor suppressors. The loss of a functional phosphatase involved in regulating growth promoting signals could lead to neoplasia. However, examples are known where dephosphorylation is required for promotion of cell growth. This is particularly true of specialized kinases that are directly involved in regulating cell cycle progression. Therefore, it is difficult to envision that all phosphatases could be tumor suppressors.
The phosphorylation and dephosphorylation of Ser, Thr, and Tyr residues in proteins do not represent the only mechanisms for the regulation of cell growth and proliferation. In addition to the numerous protein phosphatases there are families of phosphatases that are involved in the homeostasis of bioactive lipid phosphates. The actions of the various phospholipid phosphatases, like the protein phosphatases, are critical for the regulation of cell signaling events controlling growth and proliferation, metabolism, differentiation, and many other critical cellular functions.
Humans express a large number of protein phosphatases, some that are specific for phosphoserine and/or phosphothreonine, some that are specific for phosphotyrosine, and some that exhibit dual specificity. The grouping of protein phosphatases includes the HAD (haloacid dehalogenase) Asp-based phosphatase family, the Class I classical Cys-based phosphatase family, the Class II Cys-based phosphatase family, the Class III Cys-based CDC25 phosphatase family, and the serine/threonine phosphatase (PSP) family.
The HAD Asp-based phosphatase family includes the C-terminal domain (CTD) family phosphatases (8 genes) and the EYA transcriptional coactivator and phosphatases (4 genes).
The Class I classical Cys-based phosphatase family includes the dual-specificity phosphatases (six subfamilies), the protein tyrosine phosphatases non-receptor type (17 genes), and the protein tyrosine phosphatases receptor type (20 genes).
The dual-specificity phosphatase subfamilies are the MAP kinase phosphatases (11 genes), the atypical dual-specificity phosphatases (19 genes), the slingshot protein phosphatases (3 genes), the protein tyrosine phosphatase 4A family (3 genes), the CDC14 phosphatases (4 genes), and the PTEN protein phosphatases (5 genes). Although the archetype of the PTEN protein phosphatase family (PTEN: phosphatase and tensin homolog) was originally thought to be a phosphotyrosine phosphatase, it was subsequently shown to be a member of the phosphoinositide phosphatase family.
The Class II Cys-based phosphatase family consists of a single member, acid phosphatase 1, encoded by the ACP1 gene.
The Class III Cys-based CDC25 phosphatase family consists of three members, CDC25A, CDC25B, and CDC25C.
The PSP family includes members of the CTD family phosphatases, protein phosphatase catalytic subunits (13 genes), and the Mg2+/Mn2+-dependent phosphatases (18 genes).
Protein Tyrosine Phosphatases
There are two broad classes of protein tyrosine phosphatases (PTPs) divided into four families. There are at least 107 genes in the human genome that encode enzymes that belong to one or the other of the broad classes of PTP. One broad class are single pass transmembrane-spanning (transmembrane receptor-like) enzymes that contain the phosphatase activity domain in the intracellular portion of the protein. The transmembrane PTP are commonly called the receptor (RTP) class and all the genes are designated PTPR. The other broad class is intracellularly localized enzymes that are referred to as NT PTP (for non-transmembrane protein tyrosine phosphatase) and all the genes are designated PTPN.
The first transmembrane PTP characterized was the leukocyte common antigen protein, CD45. This protein was shown to have homology to the intracellular PTP identified as PTP1B. Humans express 20 genes encoding members of the RTP family. These genes encoding these enzymes are designated by the PTPR abbreviation and an additional letter of the alphabet (e.g. PTPRA and PTPRB).
There are 17 expressed human genes that encode what are referred to as classical type I non-transmembrane PTP. The designation for non-receptor tyrosine phosphatases is the abbreviation PTPN followed by an Arabic numeral (e.g. PTPN1 which was originally identified as PTP1B).
The rest of the PTP genes are defined as non-classical PTP and includes the dual-specificity phosphatases (DUSP) that are members of the MAP kinase phosphatase (MKP) family and the atypical dual-specificity phosphatases. As the name implies, DUSP can dephosphorylate tyrosine phosphate as well as serine and threonine phosphates. The are 11 genes of the MKP family which includes DUSP1 (MKP-1), DUSP2, DUSP4 (MKP-2), DUSP5, DUSP6 (MKP-3), DUSP7, DUSP8, DUSP9 (MKP-4), DUSP10 (MKP-5), DUSP16 (MKP-7), and STYXL1 (serine/threonine/tyrosine interacting like 1; also identified as DUSP24). The atypical dual-specificity phosphatase family includes 19 genes including DUSP3, 11, 12, 13A, 13B, 14, 15, 18, 19, 21, 22, 23, 26, 28, 29, EPM2A (EPM2A glucan phosphatase, laforin), PTPMT1 (protein tyrosine phosphatase mitochondrial 1), RNGTT (RNA guanylyltransferase and 5′-phosphatase), and STYX (serine/threonine/tyrosine interacting protein).
The clearest studies of a role for transmembrane PTP in signal transduction have involved the CD45 protein. These studies have shown that CD45 is involved in the regulation of the tyrosine kinase activity of LCK in T cells. LCK is associated with T cell antigens CD4 and CD8 generating a split-RTK involved in T cell activation. It is suspected that CD45 dephosphorylates a regulatory tyrosine phosphorylation site in the C-terminus of LCK, thereby, increasing the activity of LCK towards its substrate(s).
Table of Human Receptor Tyrosine Phosphatases (RTP)
| Symbol | Enzyme Name | Other Common Abbreviations |
| PTPRA | protein tyrosine phosphatase, receptor type, A | LRP, PTPA, PTPRL2 |
| PTPRB | protein tyrosine phosphatase, receptor type, B | PTPB |
| PTPRC | protein tyrosine phosphatase, receptor type, C | CD45 |
| PTPRD | protein tyrosine phosphatase, receptor type, D | PTPD |
| PTPRE | protein tyrosine phosphatase, receptor type, E | PTPE |
| PTPRF | protein tyrosine phosphatase, receptor type, F | LAR |
| PTPRG | protein tyrosine phosphatase, receptor type, G | PTPG |
| PTPRH | protein tyrosine phosphatase, receptor type, H | SAP-1 |
| PTPRJ | protein tyrosine phosphatase, receptor type, J | CD148, DEP1 |
| PTPRK | protein tyrosine phosphatase, receptor type, K | R-PTP-kappa |
| PTPRM | protein tyrosine phosphatase, receptor type, M | PTPRL1 |
| PTPRN | protein tyrosine phosphatase, receptor type, N | IA-2 |
| PTPRN2 | protein tyrosine phosphatase, receptor type, N polypeptide 2 | IA-2β, phogrin |
| PTPRO | protein tyrosine phosphatase, receptor type, O | PTPU2 |
| PTPRQ | protein tyrosine phosphatase, receptor type, Q | DFNB84 |
| PTPRR | protein tyrosine phosphatase, receptor type, R | PTPRQ, PTPBR7 |
| PTPRS | protein tyrosine phosphatase, receptor type, S | |
| PTPRT | protein tyrosine phosphatase, receptor type, T | RPTPrho |
| PTPRU | protein tyrosine phosphatase, receptor type, U | PTPRO |
| PTPRZ1 | protein tyrosine phosphatase, receptor type, Z polypeptide 1 | PTPZ, PTP18, phosphacan |
The second class of PTP are the intracellular proteins. The C-terminal residues of most, if not all, intracellular PTP are very hydrophobic and suggest these sites are membrane attachment domains of these proteins. One role of intracellular PTP is in the maturation of Xenopus oocytes in response to hormone. Over expression of PTPN1 in oocytes resulted in a marked impairment in the rate of insulin- and progesterone-induced maturation. These results suggest a role for PTPN1 in countering the signals leading to cellular activation.
Table of Classical Non-Receptor Tyrosine Phosphatases (PTPN)
| Symbol | Enzyme Name | Other Common Abbreviations |
| PTPN1 | protein tyrosine phosphatase, nonreceptor type 1 | PTP1B |
| PTPN2 | protein tyrosine phosphatase, nonreceptor type 2 | PTPT, TCPTP |
| PTPN3 | protein tyrosine phosphatase, nonreceptor type 3 | PTPH1 |
| PTPN4 | protein tyrosine phosphatase, nonreceptor type 4 (megakaryocyte) | PTPMEG |
| PTPN5 | protein tyrosine phosphatase, nonreceptor type 5 (striatum-enriched) | STEP |
| PTPN6 | protein tyrosine phosphatase, nonreceptor type 6 | PTP1C |
| PTPN7 | protein tyrosine phosphatase, nonreceptor type 7 | HEPTP |
| PTPN9 | protein tyrosine phosphatase, nonreceptor type 9 | MEG2 |
| PTPN11 | protein tyrosine phosphatase, nonreceptor type 11 | PTP2C, SHP-2, SH-PTP2 |
| PTPN12 | protein tyrosine phosphatase, nonreceptor type 12 | PTPG1 |
| PTPN13 | protein tyrosine phosphatase, nonreceptor type 13 [APO-1/CD95(Fas)-associated phosphatase] | PTP1E, PTPL1 |
| PTPN14 | protein tyrosine phosphatase, nonreceptor type 14 | PEZ |
| PTPN18 | protein tyrosine phosphatase, nonreceptor type 18 (brain-derived) | BDP1 |
| PTPN20 | protein tyrosine phosphatase, nonreceptor type 20 | PTPN20A, PTPN20B |
| PTPN21 | protein tyrosine phosphatase, nonreceptor type 21 | PTPD1, PTPRL10 |
| PTPN22 | protein tyrosine phosphatase, nonreceptor type 22 (lymphoid) | PTPN8, Lyp1, Lyp2 |
| PTPN23 | protein tyrosine phosphatase, nonreceptor type 23 | HD-PTP |
The above observation as well as several others have demonstrated a link between insulin function and PTPN1. PTPN1 directly interacts with the insulin receptor and removes the tyrosine phosphates incorporated by autophosphorylation in response to insulin binding, thereby, negatively affecting the activity of the insulin receptor. Mice lacking a functional PTPN1 gene exhibit increased insulin sensitivity as well as resistance to obesity induced by a high fat diet.
As with the transmembrane PTP little is known about the regulation of the activity of the intracellular PTP. Two intracellular PTP (PTPN6 and PTPN21) have been shown to contain SH2 domains. These SH2 domains allow these PTP to directly interact with tyrosine phosphorylated RTK and PTK, thereby, dephosphorylating tyrosines in these proteins. Following receptor stimulation of signal transduction events, the SH2 containing PTP are directed to several of the RTK and/or PTK with the net effect being a termination of the signaling events by tyrosine dephosphorylation.
Protein Serine/Threonine Phosphatases
Other phosphatases that recognize serine and/or threonine phosphorylated proteins also exist in cells. These are referred to as protein serine phosphatases (PSP). The PSP are grouped into three major families: protein phosphatase catalytic subunits (genes designated PPP), protein phosphatases Mg2+/Mn2+-dependent (genes designated PPM), and the CTD family phosphatases which are Asp-based phosphatases represented by FCP/SCP. These acronyms are derived from transcription factor IIF (TFIIF)-associating component of RNA polymerase II C-terminal domain (CTD) phosphatase/small CTD phosphatase.
Phosphoprotein Phosphatase (PPP) Family
The broad spectrum of activity associated with the members of the PPP family stems from the ability of the catalytic subunits to associate with a large variety of different regulatory/inhibitory subunits. The regulatory/inhibitory subunits are grouped into five subfamilies termed the protein phosphatase (1, 2, 3, 4, and 6) regulatory subunit families. The designations for these regulatory gene families is PPP1R, PPP2R, PPP3R, PPP4R, and PPP6R. The number of PPP regulatory subunit genes is vast with the PPP1R family being composed of 181 genes in humans, the PPP2R family composed of 15 genes, the PPP3R family composed of 2 genes, the PPP4R family composed of 3 genes, and the PPP6R family composed of 6 genes. Although there are several PPP regulatory subunit genes involved in the regulation of metabolism, the proteins encoded by the PPP1R3A and PPP1R3B genes are the most critical to the regulation of glycogen homeostasis.
Table of Human Phosphoprotein Phosphatase (PPP), Catalytic Subunits
| Symbol | Enzyme Name | Comments; Common Abbreviations |
| PPP1CA | protein phosphatase 1, catalytic subunit, alpha (α) isozyme | originally identified as PP1; PP1A, PPP1A, PP1alpha (PP1α) |
| PPP1CB | protein phosphatase 1, catalytic subunit, beta (β) isozyme | originally identified as PP1; PP1B, PP1beta (PP1β); also referred to as PP1delta (PP1δ) |
| PPP1CC | protein phosphatase 1, catalytic subunit, gamma (γ) isozyme | originally identified as PP1; PP1C, PP1gamma; two major isoforms identified as PP1Cγ1 and PP1Cγ2 |
| PPP2CA | protein phosphatase 2, catalytic subunit, alpha (α) isozyme | originally identified as PP2A; PP2Calpha (PP2Cα) |
| PPP2CB | protein phosphatase 2, catalytic subunit, beta (β) isozyme | originally identified as PP2A; PP2Abeta (PP2Aβ) |
| PPP3CA | protein phosphatase 3, catalytic subunit, alpha (α) isozyme | originally identified as PP2B or calcineurin A; PPP2B, CALN, CALNA |
| PPP3CB | protein phosphatase 3, catalytic subunit, beta (β) isozyme | originally identified as PP2B or calcineurin B; PP2Bbeta, CALNA2, CALNB |
| PPP3CC | protein phosphatase 3, catalytic subunit, gamma (γ) isozyme | originally identified as PP2B or calcineurin; PP2Bgamma, CALNA3 |
| PPP4C | protein phosphatase 4, catalytic subunit | PP4, PPX |
| PPP5C | protein phosphatase 5, catalytic subunit | PP5 |
| PPP6C | protein phosphatase 6, catalytic subunit | PP6 |
| PPEF1 | protein phosphatase, EF-hand calcium binding domain 1 | PPP7CA |
| PPEF22 | protein phosphatase, EF-hand calcium binding domain 2 | PPP7CB |
Protein Phosphatase 1 (PP1)
Protein phosphatase 1 (PP1) represents a major subfamily of protein serine/threonine phosphatases. Expression of various PP1 catalytic subunit isoforms is found in all eukaryotic cells. There are three PP1 catalytic subunit genes in humans encoding the isoforms designated PP1α (PPP1CA gene), PP1β (PPP1CB gene), and PP1γ (PPP1CC gene). All three PP1 catalytic subunit genes are subject to alternative splicing with the result that there are three isoforms derived from the PPP1CA gene, one from the PPP1CB gene (the two mRNAs from this gene encode the same protein), and two from the PPP1CC gene. The catalytic subunits of PP1 do not exist as free proteins in cells but are associated with a wide variety of regulatory/inhibitory proteins that number more than 200. The original regulatory/inhibitory protein shown to regulate the activity of PP1 was identified as inhibitor of protein phosphatase 1 (IPP-1, also identified as PPI-1). The current designation for PPI-1 is protein phosphatase 1, regulatory (inhibitory) subunit 1A, encoded by the PPP1R1A gene.
PP1 plays an important role in a wide range of cellular processes, including protein synthesis, metabolism, regulation of membrane receptors and channels, cell division, apoptosis, and reorganization of the cytoskeletal architecture. Although the many isoforms of PP1 collectively exhibit broad substrate specificity, when assembled each PP1 enzyme is believed to display highly specific substrate specificity and thus, will elicit a specific biological response. Each functional PP1 enzyme is composed of a catalytic subunit and a regulatory subunit. The catalytic subunit of PP1 is highly conserved among all eukaryotes. At least 100 putative PP1-binding regulatory subunits have been identified. The regulatory subunits are involved in targeting the PP1 catalytic subunits to specific subcellular compartments, they act to modulate substrate specificity, and they can also serve as substrates of the catalytic subunit themselves. The interactions between a given PP1 catalytic subunit and a specific regulatory subunit are central to the functions of each PP1. The catalytic subunit of PP1 contains a domain that interacts with two metal ions. This metal-binding domain is highly conserved in all members of the PPP family. The two metal ions play a role in the activation of a water molecule, which initiates a nucleophilic attack on the phosphorous atom of the substrate.
In addition to the above mentioned PPI-1, the phosphatase activity of PP1 is regulated by a number of other inhibitory proteins such as inhibitor-2 (I-2), CPI-17 (a 17 kDa PKA activated PP1 inhibitor also known as PP1 regulatory subunit 14A, PPP1R14A, found in smooth muscle and inhibits myosin light chain phosphatase, MLCP), and DARPP-32 (dopamine- and cAMP-regulated phosphoprotein 32 kDa; also known as PP1 regulatory subunit 1B, PPP1R1B). Despite the fact that there is sequence conservation between PP1 and PP2A and PP2B, the latter two phosphatases are not sensitive to inhibition by PPI-1 or I-2. It is this functional difference that was the basis for classification of type 1 (PP1) versus type 2 phosphatases.
Protein Phosphatase 2A (PP2A)
The protein phosphatases that are involved in the regulation of metabolic processes are of two types: type 1, namely the PP1 isoforms, and the type 2 isoforms, which consist of three catalytic enzymes: PP2A, PP2B, and PP2C. The phosphatase originally designated as PP2C is a member of the metal-dependent protein phosphatase (PPM) family.
PP2A exists in two distinct catalytic isoforms encoded by two genes identified as PPP2CA and PPP2CB. These PP2A isoforms play important roles in development, cell proliferation, apoptosis, cell mobility, cytoskeleton dynamics, the control of the cell cycle, and the regulation of numerous signaling pathways. PP2A isoforms represent some of the most abundant enzymes in cells and can account for up to 1% of total cellular protein in some tissues. PP2A has also been suggested to be a tumor suppressor. PP2A is highly conserved across a variety of eukaryotic species. The mechanisms of its regulatory action are highly complex.
As indicated, PP2A exists in two basic isoforms: a heterodimeric core enzyme and a heterotrimeric holoenzyme. The PP2A core enzyme consists of a scaffold subunit (originally termed the A subunit) and a catalytic subunit (the C subunits). The scaffold and the catalytic subunits each exist in two isoforms: alpha (α) and beta (β). The catalytic α subunit is encoded by the PPP2CA gene and the catalytic β subunit is encoded by the PPP2CB gene. The scaffold α subunit is encoded by the PPP2R1A gene and the β subunit by the PPP2R1B gene. The α catalytic isoform is approximately 10 times more abundant than the β isoform. The PP2A core enzyme interacts with a variable regulatory subunit to assemble into a holoenzyme. The heterotrimeric PP2A holoenzyme is believed to exhibit exquisite substrate specificity as well as spatially and temporally determined functions.
The PP2A regulatory subunits comprise four families originally classified as the B subunits (B, B’, B”, and B”’). Each family consists of multiple isoforms that are encoded by different genes. There are currently 15 different PP2A B regulatory subunit genes expressed in humans. Several of these genes generate multiple isoforms as a result of alternative splicing. Except for subunits of the B”’ family, all members of these regulatory subunit families have been shown to bind directly to the PP2A catalytic subunits. The level of expression of the various regulatory subunit genes varies greatly in different cell types and tissues. The PP2A scaffold subunits contains 15 tandem HEAT (huntingtin- elongation-A subunit-TOR) repeats. The catalytic subunits of PP2A recognize a conserved domain of HEAT repeats 1. Although other PPP family members share extensive sequence similarity with the catalytic subunit of PP2A, they do not associate with the PP2A scaffold subunits. The catalytic subunits of PP2A are targets of a number of potent tumor-inducing toxins, such as okadaic acid (OA) and microcystin-LR (MCLR). Both OA and MCLR interact with a similar set of amino acids surrounding the active site of the catalytic subunits. The major function of the PP2A regulatory subunits is to target phosphorylated substrate proteins to the phosphatase activity of the PP2A catalytic subunits.
Reversible methylation of the PP2A catalytic subunits is a conserved mechanism for the regulation of PP2A function. Methylation of leucine 309 (L309) in the C-terminus, within a conserved motif of the catalytic α subunit (the PPP2CA encoded protein), has been shown to enhance the affinity of the PP2A core enzyme for some, but not all, regulatory subunits. This implies that changes in PP2A methylation may modulate the specificity and activity of PP2A in cells. The reversible methylation of the PP2A catalytic α subunit is catalyzed by two conserved and PP2A-specific enzymes, leucine carboxyl methyltransferase (LCMT1) and PP2A methylesterase (PME-1). PME-1 catalyzes the removal of the methyl group, thus reversing the activity of LCMT1. The methylated C-terminus of the catalytic subunit may allow it to be targeted to specific cellular location for holoenzyme assembly. In addition, the methylated C-terminus may recruit other proteins that facilitate the assembly of the PP2A holoenzymes within the cell.
By analogy with the PP1 inhibitors, the endogenous inhibitors of PP2A were named I1 PP2A and I2 PP2A. The I1 PP2A inhibitor was subsequently shown to be encoded by the acidic nuclear phosphoprotein 32 family member A (ANP32A) gene which was also known as putative HLA class II-associated protein I (PHAP-I). The I2 PP2A inhibitor was subsequently shown to be encoded by the SET proto-oncogene. The name SET relates to the fact that the protein encoded by this gene was shown to have homology to three related Drosophila genes called Suppressor of variegation variant 3-9 [Su(var)3-9], Enhancer of zeste, and Trithorax. There are numerous proteins in humans that are now known to contain a similar domain now called the SET domain. Several of the SET domain-containing proteins are involved in histone methylation which alters chromatin structure and thus, gene expression.
Protein Phosphatase 2B/Calcineurin (PP2B)
Protein phosphatase 2B (PP2B, also known as calcineurin) is more correctly identified as protein phosphatase 3 (PP3). Calcineurin (PP3) plays an important role in numerous calcium-dependent biological processes that include signal transduction, immune responses, muscle development, neural development and memory, and cardiac hypertrophy. Like the other members of the PPP superfamily of serine/threonine phosphatases, calcineurin (PP3) is encoded by several catalytic subunit genes and the activity of the catalytic subunits regulated by several regulatory/inhibitory subunits.
Humans express three calcineurin catalytic subunit genes: PPP3CA (encoding the α isoform), PPP3CB (encoding the β isoform), and PPP3CC (encoding the γ isoform). There are two calcineurin (PP3) regulatory subunit genes expressed in humans identified as PPP3R1 (encoding regulatory subunit B, alpha) and PPP3R2 (encoding regulatory subunit B, beta). The catalytic subunits of calcineurin contain an N-terminal phosphatase domain, followed by a regulatory subunit-binding helical domain, a calcium (Ca2+)-calmodulin-binding motif, and an autoinhibitory element. Calcineurin is inactive alone and is active only upon association with Ca2+-calmodulin (Ca2+-CaM). The autoinhibitory element of calcineurin forms an α helix and blocks access to the catalytic site. Given this structural orientation of the catalytic site and autoinhibitory domain indicates that displacement of the autoinhibitory domain may be required for the activation of the protein.
The phosphatase domain of the catalytic subunits of calcineurin is structurally similar to the phosphatase domain of the catalytic subunits of PP1 and has the same pattern of metal ion coordination. The two metal ions associated with calcineurin are Zn2+ and Fe3+. The regulatory subunits of calcineurin contain a pair of Ca2+-binding domains forming four calcium-binding sites. All four calcium-binding sites in the regulatory subunits are bound to Ca2+ and each calcium ion is coordinated by five oxygen atoms.
The immunosuppressant complexes, FKBP12-FK506 and cyclophilin A (CyPA)-cyclosporin A (CsA) both associate with an exposed surface of the regulatory subunits of calcineurin. Binding by these immunosuppressant complexes is thought to inhibit calcineurin-mediated dephosphorylation of the transcription factor, nuclear factor of activated T cells 1 (NFAT1), ultimately resulting in the suppression of T cell activation. In both cases, the immunosuppressants make direct contacts with residues contained in the calcium-binding domains of the regulatory subunits. This observation explains why interactions between calcineurin and immunophilins strictly depend on the presence of the immunosuppressants.
Extensive studies on the interactions of calcineurin with its substrates, especially using NFAT1, have revealed a consensus recognition motif of PxIxIT (where x represents any amino acid). Variations in substrate binding affinities can be attributed to sequence variations within the PxIxIT motif in different substrates. Although the presence of the PxIxIT motif is necessary for substrate recognition, additional binding elements from the substrate are likely to be required for the specific activity of calcineurin.
Metal-Dependent Phosphatase (PPM) Family
As the name implies the PPM family is represented by protein phosphatases that are dependent upon manganese/magnesium ions (Mn2+/Mg2+), such as PPM1A (originally identified as PP2C) and the two pyruvate dehydrogenase phosphatases (PDP1 and PDP2). The PDP1 and PDP2 enzymes are unique in that they reside within the matrix of the mitochondria. Unlike the members of the PPP family, not all phosphatases of the PPM family are associated with regulatory subunits, however, they do contain additional domains and conserved sequence motifs that are involved in the determination of substrate specificity. For both the PPP and PPM families, metal ions play a catalytic and central role through the activation of a water molecule for the dephosphorylation reaction. The PPM family includes 17 genes expressed in humans. The two pyruvate dehydrogenase phosphatases (PDP1 and PDP2) do interact with a regulatory subunit which is encoded by the PDPR gene.
Protein Phosphatase 2C Family (PP2C: PPM)
Protein phosphatase 2C actually represents a subfamily (PPM1) of the Mn2+/Mg2+-dependent PPM family of protein phosphatases. The PPM family represents a large family of highly conserved protein phosphatases, with 17 distinct PPM encoding genes in the human genome that give rise to at least 22 different isoforms. The PPM1 (originally identified as PP2C) subfamily consists of 12 genes. Two additional, highly important metabolic regulating enzymes of the PPM family are the pyruvate dehydrogenase phosphatases. The different PPM isoforms exhibit distinct functions, expression patterns, and subcellular localization.
Unlike the PPP family phosphatases, PPM family phosphatases are insensitive to inhibition by okadaic acid or microcystin. The primary function of PPM1 subfamily phosphatase is in the regulation of cellular stress signaling, and they also play roles in the regulation of metabolism, differentiation, growth, survival, and apoptosis. Several members of the PPM family are candidate tumor suppressor proteins. These include PPM1A (originally called PP2Cα), PPM1B (originally called PP2Cβ), and the plextrin homology (PH) domain leucine-rich repeat protein phosphatases (PHLPP1 and PHLPP2). On the other hand PPM1D (originally identified as PP2Cδ and Wip1) may contribute to oncogenic transformation.
The conserved catalytic domain of human PPM enzymes contains a central β-sandwich, with each β-sheet flanked by a pair of α-helices, the orientation of which generates a cleft between the two β-sheets. The two metal ions are found at the base of the cleft with each metal ion hexacoordinated by amino acids and water molecules. The catalytic activity of PPM phosphatases is similar to that of the PPP family. The dephosphorylation reaction involves nucleophilic attack of the phosphorous by a metal-activated water nucleophile.
Table of Human PPM Family Phosphatases
| Symbol | Enzyme Name | Other Common Abbreviations |
| PPM1A | protein phosphatase, Mg2+/Mn2+ dependent, 1A | PP2CA, PP2Calpha |
| PPM1B | protein phosphatase, Mg2+/Mn2+ dependent, 1B | PP2CB, PP2Cbeta |
| PPM1D | protein phosphatase, Mg2+/Mn2+ dependent, 1D | PP2Cdelta, Wip1 |
| PPM1E | protein phosphatase, Mg2+/Mn2+ dependent, 1E | PP2CH, CaMKP-N, POPX1 |
| PPM1F | protein phosphatase, Mg2+/Mn2+ dependent, 1F | CaMKPase, CAMKP, POPX2 |
| PPM1G | protein phosphatase, Mg2+/Mn2+ dependent, 1G | PP2CG, PP2Cgamma |
| PPM1H | protein phosphatase, Mg2+/Mn2+ dependent, 1H | ARHCL1 |
| PPM1J | protein phosphatase, Mg2+/Mn2+ dependent, 1J | PP2CZ, PP2Czeta |
| PPM1K | protein phosphatase, Mg2+/Mn2+ dependent, 1K | PP2Ckappa, PP2Cm |
| PPM1L | protein phosphatase, Mg2+/Mn2+ dependent, 1L | PP2CE |
| PPM1M | protein phosphatase, Mg2+/Mn2+ dependent, 1M | P2Ceta6 |
| PPM1N | protein phosphatase, Mg2+/Mn2+ dependent, 1N | |
| PDP1 | pyruvate dehydrogense phosphatase catalytic subunit 1 | PPM2C, PDP |
| PDP2 | pyruvate dehydrogense phosphatase catalytic subunit 2 | PPM2C2 |
| PHLPP1 | PH domain and leucine rich repeat protein phosphatase 1 | PHLPP, SCOP |
| PHLPP2 | PH domain and leucine rich repeat protein phosphatase 1 | PHLPPL |
| ILKAP | integrin-linked kinase-associated serine/threonine phosphatase |
Aspartate-Based Phosphatase (FCP/SCP) Family
In contrast to the mechanism of action of the PPP and PPM phosphatases, the FCP/SCP phosphatases use an aspartate-based catalytic mechanism. There is currently only one known substrate for FCP/SCP and as the name implies it is the C-terminal domain (CTD) of RNA polymerase II. The CTD of RNA polymerase II contains tandem repeats of a serine-rich heptapeptide and the state of phosphorylation of several serines in this repeat is critical for the regulation of polymerase activity (see the RNA: Transcription and Processing page for more details). The conserved structural core of FCP/SCP is the FCP homology (FCPH) domain. FCP, but not SCP, also contain a BRCA1 C-terminal domain-like (BRCT) domain that is C-terminal to the FCPH domain.
The phosphatases that are members of the FCP/SCP family utilize the aspartic acids of the sequence motif DxDxT/V for phosphatase activity. The FCP/SCP phosphatase family was originally identified as being exclusive to the dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II. The CTD of RNA polymerase II contains tandem repeats of the sequence YSPTSPS. However, it is now known that there are many other substrates for the action of these phosphatases such as in the dephosphorylation of Smad proteins. There are eight putative CTD phosphatases in the human genome. The original FCP and SCP proteins are encoded by the CTDP1 and CTDSP1 genes, respectively. The core structure of the FCP/SCP phosphatases resembles phosphoserine phosphatases from several different bacteria, the hexose phosphate phosphatase from Bacteroides (a common human intestinal bacterium), and the haloacid dehalogenase (HAD) from Xanthobacter autotrophicus.
The level, as well as the pattern of phosphorylation in the CTD repeat changes throughout the cycles of transcription, with hypophosphorylation in the preinitiation complex and hyperphosphorylation during transcription elongation. Phosphorylated serine 5 (pSer5), the serine at the fifth position in the tandem repeat, is enriched at transcription initiation and early transcription elongation, whereas phosphorylation of the serine at the second position in the tandem repeat (pSer2) is favored during transcription elongation and through the end of transcription (see the RNA: Transcription and Processing page for additional information). Fcp1 is the main serine phosphatase for the CTD. This phosphatase can dephosphorylate both pSer2 and pSer5. By comparison, Scp1 exhibits little activity for pSer2 and prefers pSer5 by a factor of 70-fold.
The catalytic mechanism of Fcp1/Scp1 likely involves two sequential steps. First, an oxygen atom from the N-terminal aspartate in the DxDxT motif initiates a nucleophilic attack on the phosphorous atom of a pSer. Second, a water nucleophile, likely activated by the second aspartate in the DxDxT motif, attacks the phosphorous atom releasing an inorganic phosphate. The Mg2+ ion likely facilitates both of these steps in the reaction by neutralizing the negative charges of the phosphate group. Of note is the fact that the role of the Mg2+ ion in Fcp1/Scp1 is different from that in the PPP or PPM family, where the metal ions are directly involved in catalysis through the activation of a water nucleophile.
Chronophin, a member of the HAD family, is also an aspartate-based PSP. Like FCP/SCP, it contains the signature sequence motif DxDxT and has a similar active site. Also, like FCP/SCP, chronophin has only one known substrate protein. Chronophin dephosphorylates pSer3 of cofilin, which is an important regulator of actin dynamics, leading to its activation.
Phospholipid Phosphatases
Enzymes that phosphorylate lipids, predominantly membrane-associated lipids, are referred to as lipid kinases with phosphatidylinositol 3-kinase (PI3K) being a well known example. As for the regulation of protein function by phosphorylation and dephosphorylation, the functions of many membrane and extracellular lipids are regulated by phosphorylation and dephosphorylation. There are a large number of lipid kinases and phospholipid phosphatases with many being discussed in greater detail in the Signal Transduction Pathways: Phospholipids page.