Summary: PAP2 superfamily
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PAP2 superfamily Provide feedback
This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. 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.
Literature references
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Stukey J, Carman GM; , Protein Sci 1997;6:469-472.: Identification of a novel phosphatase sequence motif. PUBMED:9041652 EPMC:9041652
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Neuwald AF; , Protein Sci 1997;6:1764-1767.: An unexpected structural relationship between integral membrane phosphatases and soluble haloperoxidases. PUBMED:9260289 EPMC:9260289
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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
SCOOP: | DAGK_prokar DUF212 PAP2_3 PAP2_C Scs3p UbiA |
Similarity to PfamA using HHSearch: | DUF212 PAP2_C PAP2_3 |
External database links
HOMSTRAD: | PAP2 |
PROSITE: | PDOC00891 |
SCOP: | 1d2t |
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.
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 pap2 (CL0525), which has the following description:
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:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. 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 5 members:
DUF212 PAP2 PAP2_3 PAP2_C Scs3pAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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.
Seed (75) |
Full (27867) |
Representative proteomes | UniProt (69344) |
NCBI (109066) |
Meta (1514) |
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RP15 (6049) |
RP35 (16401) |
RP55 (26412) |
RP75 (37463) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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.
Seed (75) |
Full (27867) |
Representative proteomes | UniProt (69344) |
NCBI (109066) |
Meta (1514) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (6049) |
RP35 (16401) |
RP55 (26412) |
RP75 (37463) |
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Raw Stockholm | |||||||||
Gzipped |
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...
Trees
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
Seed source: | Pfam-B_486 (release 4.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bashton M |
Number in seed: | 75 |
Number in full: | 27867 |
Average length of the domain: | 128.80 aa |
Average identity of full alignment: | 19 % |
Average coverage of the sequence by the domain: | 43.26 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 136 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
PAP2Structures
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 43 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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