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Short answer: a protein phosphatase is an enzyme that removes phosphate groups from other proteins. Kinases add phosphate and phosphatases take it off, and together they make protein phosphorylation reversible. What a phosphatase does in a given cell depends on which family it belongs to and which phosphorylated residues it acts on.
Definition and scope
Protein phosphorylation is reversible because two opposing enzyme classes act on it: as Shi puts it, “the reversible phosphorylation of proteins is accomplished by opposing activities of kinases and phosphatases” (Cell, 2009). A protein phosphatase is the second half of that pair. Tonks describes kinases and phosphatases as playing essential, competing roles in determining how a cell responds to a signal (FEBS J, 2013), which is why a phosphatase should not be pictured as a simple “off switch”: it is one side of a balance.
This page is about the enzymes that act on proteins. It does not cover alkaline phosphatase as a detection label, which is a different use of the word and is handled under secondary antibodies in western blotting and in the ELISpot assay guide.
What does a phosphatase do?
Phosphatases remove phosphate groups from proteins that kinases have phosphorylated, which returns the protein to its unphosphorylated state. Two details from the primary literature explain why this matters in practice.
- A small set of Ser/Thr phosphatases covers a very large set of substrates. Shi reports that relatively few serine/threonine phosphatases dephosphorylate thousands of substrates (Shi, 2009), whereas humans have more than 500 genes encoding protein kinases (Swingle and Honkanen, 2019).
- Specificity is often supplied by partners, not by the catalytic core. PP1 and PP2A combine conserved catalytic subunits with many different regulatory subunits, which is how a few catalytic enzymes reach many targets. PP2C and the FCP/SCP phosphatases instead carry catalytic and regulatory domains in a single polypeptide (Shi, 2009).
Main families: PPP, PPM and PTP
Protein phosphatases are grouped by the residue they act on and by their catalytic chemistry. The table summarises the three reviews listed under Sources.
| Family | Acts on | What the sources say |
|---|---|---|
| PPP | Serine / threonine | One of the two major Ser/Thr families. PP1, PP2A and PP2B (calcineurin) are the founding members and share a common catalytic mechanism (Swingle and Honkanen, 2019). PP1 and PP2A pair conserved catalytic subunits with many regulatory subunits (Shi, 2009). |
| PPM | Serine / threonine | The second major Ser/Thr family (Swingle and Honkanen, 2019). PP2C carries its catalytic and regulatory domains in one polypeptide (Shi, 2009). |
| PTP (including DUSPs) | Phosphotyrosine (classical PTPs) and dual-specificity phosphatases (DUSPs) | Roughly 100 PTP genes in humans, about 37 of which encode phosphotyrosine-specific enzymes. PTPs are cysteine-dependent enzymes that evolved independently three times; the classical phosphotyrosine-specific PTPs and the dual-specificity phosphatases (DUSPs) form the largest group (Tonks, 2013). |
Protein phosphatases versus kinases
The counts above show an asymmetry that is useful to remember. There are more than 500 human kinase genes, while the Ser/Thr phosphatases are a much smaller group working through regulatory subunits. Because the phosphatase counts quoted in the literature are not specific to humans, this page does not turn the comparison into a ratio.
Where it matters in the lab
The practical consequence is that phosphorylation state is not fixed once a sample is taken: any active phosphatase can remove the phosphate you are trying to measure. A short checklist, each point tied to a source:
- Identify the residue first. Phosphotyrosine and phosphoserine/phosphothreonine are handled by different families (PTP versus PPP/PPM), and the inhibitor literature is organised the same way: Tonks reviews the PTPs, while Swingle and Honkanen review inhibitors of the Ser/Thr phosphatases separately.
- Know that tyrosine phosphatase inhibition has a long-standing tool. Vanadate is recognised as a PTP inhibitor and is still used (Tonks, 2013).
- Check your blocking agent when you probe phosphoproteins. The reasoning for avoiding milk when detecting phosphoproteins is covered in BSA versus milk as a western blot blocking buffer.
- Read the result in context. See how to interpret western blot results for what a phospho-specific band can and cannot tell you, and what proteomics is for the wider field that maps phosphorylation across proteins.
Common misunderstandings
- “Phosphatase” does not always mean a protein phosphatase. In ELISA and western blotting, alkaline phosphatase is usually the enzyme attached to a detection antibody. See the ELISA protocol guide for that use.
- Phosphatases are not one family with one ancestor. The PTPs evolved independently three times (Tonks, 2013), and the Ser/Thr phosphatases split into the separate PPP and PPM families.
- Phosphatases are not just “off switches”. Because kinases and phosphatases compete, the net phosphorylation state reflects both activities (Tonks, 2013).
FAQ
What does a phosphatase do?
A protein phosphatase removes phosphate groups from proteins, reversing the action of kinases. This is how phosphorylation, which can change a protein’s activity, becomes reversible.
What does phosphatase do in the cell?
It sets the balance of protein phosphorylation against kinases, which together determine how a cell responds to signals. A relatively small number of Ser/Thr phosphatases act on thousands of substrates, often through regulatory subunits.
What are protein phosphatases?
They are the enzymes that dephosphorylate proteins. They fall into the Ser/Thr families PPP and PPM and the protein tyrosine phosphatase (PTP) family, which in humans comprises about 100 genes.
Sources
Full links below were checked on 2026-10-29.
- Shi Y. Serine/threonine phosphatases: mechanism through structure. Cell 2009;139(3):468-484. https://pubmed.ncbi.nlm.nih.gov/19879837/. Checked 2026-10-29.
- Tonks NK. Protein tyrosine phosphatases: from housekeeping enzymes to master regulators of signal transduction. FEBS J 2013;280(2):346-378. https://pmc.ncbi.nlm.nih.gov/articles/PMC3662559. Checked 2026-10-29.
- Swingle MR, Honkanen RE. Inhibitors of serine/threonine protein phosphatases. Curr Med Chem 2019;26(15):2634-2660. https://pmc.ncbi.nlm.nih.gov/articles/PMC10013172. Checked 2026-10-29.
