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4  structures 1228  species 0  interactions 2990  sequences 86  architectures

Family: P5-ATPase (PF12409)

Summary: P5-type ATPase cation transporter

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P5-type ATPase cation transporter Provide feedback

This domain family is found in eukaryotes, and is typically between 110 and 126 amino acids in length. The family is found in association with PF00122 PF00702. P-type ATPases comprise a large superfamily of proteins, present in both prokaryotes and eukaryotes, that transport inorganic cations and other substrates across cell membranes.

Literature references

  1. Schultheis PJ, Hagen TT, O'Toole KK, Tachibana A, Burke CR, McGill DL, Okunade GW, Shull GE;, Biochem Biophys Res Commun. 2004;323:731-738.: Characterization of the P5 subfamily of P-type transport ATPases in mice. PUBMED:15381061 EPMC:15381061

This tab holds annotation information from the InterPro database.

InterPro entry IPR006544

P-ATPases (also known as E1-E2 ATPases) ([intenz:3.6.3.-]) are found in bacteria and in a number of eukaryotic plasma membranes and organelles [ PUBMED:9419228 ]. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H + , Na + , K + , Mg 2+ , Ca 2+ , Ag + and Ag 2+ , Zn 2+ , Co 2+ , Pb 2+ , Ni 2+ , Cd 2+ , Cu + and Cu 2+ . P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

There are several different types of transmembrane ATPases, which can differ in function (ATP hydrolysis and/or synthesis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [ PUBMED:15473999 , PUBMED:15078220 ]. The different types include:

  • F-ATPases (ATP synthases, F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts).
  • V-ATPases (V1V0-ATPases), which are primarily found in eukaryotes and they function as proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane [ PUBMED:20450191 ]. They are also found in bacteria [ PUBMED:9741106 ].
  • A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases, though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases [ PUBMED:18937357 , PUBMED:1385979 ].
  • P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes.
  • E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.

These P-type ATPases from eukaryotes form a different clade, designated subfamily V [ PUBMED:9419228 ]. P-type ATPases use ATP for intracellular cation homeostasis and are required for proper lysosomal and mitochondria maintenance [ PUBMED:32973005 ], also playing a role in the maintenance of neuronal integrity [ PUBMED:27278822 ]. P-type ATPases are also involved in the uptake and/or transport of polyamines, contributing to the polyamines homeostasis within the cells [ PUBMED:19762559 ].

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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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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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: P_ATPase;
Type: Family
Sequence Ontology: SO:0100021
Author: Gavin OL
Number in seed: 139
Number in full: 2990
Average length of the domain: 123.8 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 10.44 %

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 22.7 22.7
Trusted cut-off 22.7 22.9
Noise cut-off 22.6 22.6
Model length: 126
Family (HMM) version: 11
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 P5-ATPase domain has been found. There are 4 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
A0A044TXN6 View 3D Structure Click here
A0A077YZL0 View 3D Structure Click here
A0A0D2GSQ0 View 3D Structure Click here
A0A0K0E871 View 3D Structure Click here
A0A0K0EAT2 View 3D Structure Click here
A0A0N4UH06 View 3D Structure Click here
A0A175WDK6 View 3D Structure Click here
A0A1C1D1W2 View 3D Structure Click here
A0A1D8PGL4 View 3D Structure Click here
A0A2R8QKM0 View 3D Structure Click here
A0A3P7DE29 View 3D Structure Click here
A0A5K4F0A3 View 3D Structure Click here
A0A5K4F4Z6 View 3D Structure Click here
A0A5K4F5E8 View 3D Structure Click here
A0A5S6PFM4 View 3D Structure Click here
A8DZ26 View 3D Structure Click here
C0NE87 View 3D Structure Click here
C1HD57 View 3D Structure Click here
F1M9L4 View 3D Structure Click here
F1MA70 View 3D Structure Click here
F1MAA4 View 3D Structure Click here
G3V677 View 3D Structure Click here
M0RAB1 View 3D Structure Click here
O14022 View 3D Structure Click here
O74431 View 3D Structure Click here
Q12697 View 3D Structure Click here
Q21286 View 3D Structure Click here
Q27533 View 3D Structure Click here
Q3TYU2 View 3D Structure Click here
Q4VNC0 View 3D Structure Click here
Q4VNC1 View 3D Structure Click here
Q54NW5 View 3D Structure Click here
Q54P22 View 3D Structure Click here
Q54X63 View 3D Structure Click here
Q5XF89 View 3D Structure Click here
Q5XF90 View 3D Structure Click here
Q5ZKB7 View 3D Structure Click here
Q8I3U7 View 3D Structure Click here
Q95JN5 View 3D Structure Click here
Q9CTG6 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;