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106  structures 2078  species 0  interactions 41309  sequences 745  architectures

Family: PP2C (PF00481)

Summary: Protein phosphatase 2C

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Protein phosphatase 2C Provide feedback

Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase.

Literature references

  1. Das AK, Helps NR, Cohen PT, Barford D; , EMBO J 1996;15:6798-6809.: Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution. PUBMED:9003755 EPMC:9003755

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001932

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 Mg2- or Mn2-dependent (PPM) families. The core structure of PPMs is the 300-residue PPM-type phosphatase domain that catalyses 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 [ PUBMED:9003755 , PUBMED:9869399 , PUBMED:22115775 , PUBMED:22668558 ].

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 governed 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 catalysing 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 beta-strands and 5 segments of alpha-helix and comprises a pair of detached subdomains. The first is a small beta-sandwich with strand beta1 packed against strands beta2 and beta3; the second is a larger beta-sandwich in which a four-stranded beta-sheet packs against a three-stranded beta-sheet with flanking alpha-helices [ PUBMED:9003755 , PUBMED:22115775 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PP2C (CL0238), which has the following description:

This clan includes the PP2C family of phosphatases as well as the SpoIIE family. This suggests SpoIIE proteins may also be phosphatases.

The clan contains the following 3 members:



We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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Representative proteomes UniProt

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Finn RD
Number in seed: 28
Number in full: 41309
Average length of the domain: 220.1 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 48.07 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 258
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PP2C domain has been found. There are 106 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044QRY4 View 3D Structure Click here
A0A044RZI8 View 3D Structure Click here
A0A044SU30 View 3D Structure Click here
A0A044SU44 View 3D Structure Click here
A0A044TAH4 View 3D Structure Click here
A0A044UNN7 View 3D Structure Click here
A0A044UYZ0 View 3D Structure Click here
A0A044V4H2 View 3D Structure Click here
A0A044V6V9 View 3D Structure Click here
A0A044V9P2 View 3D Structure Click here
A0A060D932 View 3D Structure Click here
A0A075T3H0 View 3D Structure Click here
A0A075T8J6 View 3D Structure Click here
A0A075T8K1 View 3D Structure Click here
A0A077Z151 View 3D Structure Click here
A0A077Z3D1 View 3D Structure Click here
A0A077Z6F0 View 3D Structure Click here
A0A077Z8C2 View 3D Structure Click here
A0A077ZBJ3 View 3D Structure Click here
A0A077ZG77 View 3D Structure Click here
A0A077ZHG7 View 3D Structure Click here
A0A096T5F5 View 3D Structure Click here
A0A0A2V6R0 View 3D Structure Click here
A0A0B4J374 View 3D Structure Click here
A0A0D2GAX9 View 3D Structure Click here
A0A0D2GJ02 View 3D Structure Click here
A0A0D2GLA9 View 3D Structure Click here
A0A0D2GZW9 View 3D Structure Click here
A0A0D2HDP1 View 3D Structure Click here
A0A0I9N7S9 View 3D Structure Click here
A0A0K0DTM9 View 3D Structure Click here
A0A0K0DXI6 View 3D Structure Click here
A0A0K0E1S6 View 3D Structure Click here
A0A0K0E7I7 View 3D Structure Click here
A0A0K0E8Z3 View 3D Structure Click here
A0A0K0EL04 View 3D Structure Click here
A0A0K0JBT9 View 3D Structure Click here
A0A0K0JCW7 View 3D Structure Click here
A0A0N4U1V3 View 3D Structure Click here
A0A0N4U4Q7 View 3D Structure Click here