PROSITE documentation PDOC00792
PPM-type phosphatase domain signature and profile


Protein phosphatases remove phosphate groups from various proteins that are the key components of a number of signalling pathways in eukaryotes and prokaryotes. Protein phosphatases that dephosphorylate Ser and Thr residues are classified into the phosphoprotein (PPP) and the protein phosphatase Mg(2+)- or Mn(2+)-dependent (PPM) families. The core structure of PPMs is the 300-residue PPM-type phosphatase domain that catalyzes the dephosphorylation of phosphoserine- and phosphothreonine-containing protein. The PPM-type phosphatase domain is found as a module in diverse structural contexts and is modulated by targeting and regulatory subunits [1,2,3,4].

Some proteins known to contain a PPM-type phosphatase domain are listed below:

  • Bacillus subtilis stage II sporulation protein E (SpoIIE), controls the sporulation by dephosphorylating an anti-transcription factor SpoIIAA, reversing the actions of the SpoIIAB protein kinase in a process that is gouverned by the ADP/ATP ratio [levdikov].
  • Mycobacterium tuberculosis PP2C-family Ser/Thr phosphatase (PstP).
  • Eucaryotic PP2C, a negative regulator of protein kinase cascades that are activated as a result of stress.
  • Yeast adenyl cyclase, plays essential roles in regulation of cellular metabolism by catalyzing the synthesis of a second messenger, cAMP.
  • Mammalian mitochondrial pyruvate dehydrogenase phosphatase 1 (PDP1).
  • Plant kinase-associated protein phosphatase (KAPP), regulates receptor-like kinase (RLK) signalling pathways.
  • Plant absissic acid-insenstive 1 and 2 (ABI1 and ABI2), play a key absissic acid (ABA) signal transduction.

The PP2C-type phosphatase domain consists of 10 segments of β-strands and 5 segments of α-helix and comprises a pair of detached subdomains. The first is a small β-sandwich with strand β1 packed against strands β2 and β3; the second is a larger β-sandwich in which a four-stranded β-heet packs against a three-stranded β-sheet with flanking α-helices (see <PDB:3T9Q>) [1,3].

As a signature pattern, we selected the best conserved region which is located in the N-terminal part and contains a perfectly conserved tripeptide. This region includes a conserved aspartate residue involved in divalent cation binding [1]. We also developed a profile that covers the entire PPM-type phosphatase domain.

Last update:

February 2015 / Text revised; profile added.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

PPM_2, PS51746; PPM-type phosphatase domain profile  (MATRIX)

PPM_1, PS01032; PPM-type phosphatase domain signature  (PATTERN)


1AuthorsDas A.K. Helps N.R. Cohen P.T.W. Barford D.
TitleCrystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution.
SourceEMBO J. 15:6798-6809(1996).
PubMed ID9003755

2AuthorsRodriguez P.L.
TitleProtein phosphatase 2C (PP2C) function in higher plants.
SourcePlant Mol. Biol. 38:919-927(1998).
PubMed ID9869399

3AuthorsLevdikov V.M. Blagova E.V. Rawlings A.E. Jameson K. Tunaley J. Hart D.J. Barak I. Wilkinson A.J.
TitleStructure of the phosphatase domain of the cell fate determinant SpoIIE from Bacillus subtilis.
SourceJ. Mol. Biol. 415:343-358(2012).
PubMed ID22115775

4AuthorsMori Y. Takegawa K. Kimura Y.
TitleFunction analysis of conserved amino acid residues in a Mn(2+)-dependent protein phosphatase, Pph3, from Myxococcus xanthus.
SourceJ. Biochem. 152:269-274(2012).
PubMed ID22668558

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