Summary: PAP2 superfamily
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
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.
PAP2 superfamily Provide feedback
This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:18.104.22.168, Phosphatidylglycerophosphatase B EC:22.214.171.124 and bacterial acid phosphatase EC:126.96.36.199. The family also includes a variety of haloperoxidases [1,2] that function by oxidising halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.
Messerschmidt A, Wever R; , Proc Natl Acad Sci U S A 1996;93:392-396.: X-ray structure of a vanadium-containing enzyme: chloroperoxidase from the fungus Curvularia inaequalis. PUBMED:8552646 EPMC:8552646
Internal database links
|Similarity to PfamA using HHSearch:||DUF212 PAP2_C PAP2_3|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000326
This entry represents type 2 phosphatidic acid phosphatase (PAP2; EC) enzymes, such as phosphatidylglycerophosphatase B EC from Escherichia coli. PAP2 enzymes have a core structure consisting of a 5-helical bundle, where the beginning of the third helix binds the cofactor [PUBMED:10835340]. PAP2 enzymes catalyse the dephosphorylation of phosphatidate, yielding diacylglycerol and inorganic phosphate [PUBMED:17079146]. In eukaryotic cells, PAP activity has a central role in the synthesis of phospholipids and triacylglycerol through its product diacylglycerol, and it also generates and/or degrades lipid-signalling molecules that are related to phosphatidate.
Other related enzymes have a similar core structure, including haloperoxidases such as bromoperoxidase (contains one core bundle, but forms a dimer), chloroperoxidases (contains two core bundles arranged as in other family dimers), bacitracin transport permease from Bacillus licheniformis, glucose-6-phosphatase from rat. The vanadium-dependent haloperoxidases exclusively catalyse the oxidation of halides, and act as histidine phosphatases, using histidine for the nucleophilic attack in the first step of the reaction [PUBMED:12447906]. Amino acid residues involved in binding phosphate/vanadate are conserved between the two families, supporting a proposal that vanadium passes through a tetrahedral intermediate during the reaction mechanism.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|Molecular function||catalytic activity (GO:0003824)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
The PAP2 superfamily is characterised by being mult-helical, with the core consisting of a 5-helical bundle. Normally the family will bind cofactor at the beginning of the third helix. The superfamily includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:188.8.131.52, Phosphatidylglycerophosphatase B EC:184.108.40.206 and bacterial acid phosphatase EC:220.127.116.11. The family also includes a variety of haloperoxidases [1,2] that function by oxidising halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.
The clan contains the following 3 members:PAP2 PAP2_3 PAP2_C
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Pfam-B_486 (release 4.0)|
|Author:||Bashton M, Bateman A|
|Number in seed:||142|
|Number in full:||14398|
|Average length of the domain:||132.00 aa|
|Average identity of full alignment:||19 %|
|Average coverage of the sequence by the domain:||47.04 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 PAP2 domain has been found. There are 44 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 seqence.
Loading structure mapping...