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676  structures 1896  species 0  interactions 52412  sequences 872  architectures

Family: Y_phosphatase (PF00102)

Summary: Protein-tyrosine phosphatase

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This is the Wikipedia entry entitled "Protein tyrosine phosphatase". More...

Protein tyrosine phosphatase Edit Wikipedia article

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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-tyrosine phosphatase Provide feedback

No Pfam abstract.

Literature references

  1. Hof P, Pluskey S, Dhe-Paganon S, Eck MJ, Shoelson SE; , Cell 1998;92:441-450.: Crystal structure of the tyrosine phosphatase SHP-2. PUBMED:9491886 EPMC:9491886

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000242

Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; EC ) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [ PUBMED:9818190 , PUBMED:14625689 ]. The PTP superfamily can be divided into four subfamilies [ PUBMED:12678841 ]:

  • (1) pTyr-specific phosphatases
  • (2) dual specificity phosphatases (dTyr and dSer/dThr)
  • (3) Cdc25 phosphatases (dTyr and/or dThr)
  • (4) LMW (low molecular weight) phosphatases

Based on their cellular localisation, PTPases are also classified as:

  • Receptor-like, which are transmembrane receptors that contain PTPase domains [ PUBMED:16672235 ]
  • Non-receptor (intracellular) PTPases [ PUBMED:8948575 ]

All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif [ PUBMED:9646865 ]. Functional diversity between PTPases is endowed by regulatory domains and subunits.

This entry represents the PTPase domain found in several tyrosine-specific protein phosphatases (PTPases).

Structurally, all known receptor PTPases, are made up of a variable length extracellular domain, followed by a transmembrane region and a C-terminal catalytic cytoplasmic domain. Some of the receptor PTPases contain fibronectin type III (FN-III) repeats, immunoglobulin-like domains, MAM domains or carbonic anhydrase-like domains in their extracellular region. The cytoplasmic region generally contains two copies of the PTPase domain. The first seems to have enzymatic activity, while the second is inactive. The inactive domains of tandem phosphatases can be divided into two classes. Those which bind phosphorylated tyrosine residues may recruit multi-phosphorylated substrates for the adjacent active domains and are more conserved, while the other class have accumulated several variable amino acid substitutions and have a complete loss of tyrosine binding capability. The second class shows a release of evolutionary constraint for the sites around the catalytic centre, which emphasises a difference in function from the first group. There is a region of higher conservation common to both classes, suggesting a new regulatory centre [ PUBMED:14739250 ]. PTPase domains consist of about 300 amino acids. There are two conserved cysteines, the second one has been shown to be absolutely required for activity. Furthermore, a number of conserved residues in its immediate vicinity have also been shown to be important.

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 Phosphatase (CL0031), which has the following description:

This family includes tyrosine and dual specificity phosphatase enzymes.

The clan contains the following 16 members:

BLH_phosphatase CDKN3 DSPc DSPn Init_tRNA_PT LMWPc Myotub-related NleF_casp_inhib PTPlike_phytase PTS_IIB Rhodanese Ssu72 Syja_N Y_phosphatase Y_phosphatase2 Y_phosphatase3


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.

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Representative proteomes UniProt

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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: Swissprot_feature_table
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL , Griffiths-Jones SR
Number in seed: 90
Number in full: 52412
Average length of the domain: 213.20 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 30.32 %

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 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 235
Family (HMM) version: 30
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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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 Y_phosphatase domain has been found. There are 676 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
A0A0G2JXZ9 View 3D Structure Click here
A0A0G2K2N0 View 3D Structure Click here
A0A0G2K2W0 View 3D Structure Click here
A0A0G2K754 View 3D Structure Click here
A0A0G2KFA2 View 3D Structure Click here
A0A0H2UKT5 View 3D Structure Click here
A0A0R0ENX4 View 3D Structure Click here
A0A0R4I9I3 View 3D Structure Click here
A0A0R4IER5 View 3D Structure Click here
A0A0R4IPR0 View 3D Structure Click here
A0A0R4ITJ9 View 3D Structure Click here
A0A1B1LZI1 View 3D Structure Click here
A0A1D6EHC5 View 3D Structure Click here
A0A1D6MYT0 View 3D Structure Click here
A0A1D8PLX9 View 3D Structure Click here
A0A1D8PU75 View 3D Structure Click here
A0A1L1QZV5 View 3D Structure Click here
A0A286Y7Z0 View 3D Structure Click here
A0A286Y832 View 3D Structure Click here
A0A286YB50 View 3D Structure Click here
A0A286YBL8 View 3D Structure Click here
A0A2R8Q2T0 View 3D Structure Click here
A0A2R8Q7H4 View 3D Structure Click here
A0A2R8QCZ8 View 3D Structure Click here
A0A2R8QL35 View 3D Structure Click here
A0A2R8QLE2 View 3D Structure Click here
A0A2R8RL72 View 3D Structure Click here
A0A2R8RLA8 View 3D Structure Click here
A1L1L3 View 3D Structure Click here
A1ZAB3 View 3D Structure Click here
A2A8L5 View 3D Structure Click here
A2ALK8 View 3D Structure Click here
A3KPJ4 View 3D Structure Click here
A4HWS2 View 3D Structure Click here
A4HWS4 View 3D Structure Click here
A4IDJ2 View 3D Structure Click here
A4IDV1 View 3D Structure Click here
A4IFW2 View 3D Structure Click here
A5I9F0 View 3D Structure Click here
A8DZA4 View 3D Structure Click here