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5  structures 3394  species 0  interactions 10726  sequences 127  architectures

Family: Patatin (PF01734)

Summary: Patatin-like phospholipase

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This is the Wikipedia entry entitled "Patatin-like phospholipase". More...

Patatin-like phospholipase Edit Wikipedia article

1oxw opm.gif
Patatin
Identifiers
Symbol Patatin
Pfam PF01734
InterPro IPR002641
PROSITE PDOC00951
SCOP 1oxw
SUPERFAMILY 1oxw
OPM superfamily 134
OPM protein 1oxw

Family of patatin-like phospholipases consists of various patatin glycoproteins from the total soluble protein from potato tubers,[1] and also some proteins found in vertebrates. Patatin is a storage protein but it also has the enzymatic activity of phospholipase, catalysing the cleavage of fatty acids from membrane lipids.[1]

[edit] Subfamilies

  • Protein of unknown function UPF0028 IPR001423

[edit] Human proteins containing this domain

PNPLA1; PNPLA2; PNPLA4; PNPLA5; PNPLA6; PNPLA7; PNPLA8;

[edit] References

  1. ^ a b Mignery GA, Pikaard CS, Park WD (1988). "Molecular characterization of the patatin multigene family of potato". Gene 62 (1): 27–44. doi:10.1016/0378-1119(88)90577-X. PMID 3371664.

This article incorporates text from the public domain Pfam and InterPro IPR002641

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Patatin-like phospholipase Provide feedback

This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers [2]. Patatin is a storage protein but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids [2]. Members of this family have been found also in vertebrates.

Literature references

  1. Banfalvi Z, Kostyal Z, Barta E; , Mol Gen Genet 1994;245:517-522.: Solanum brevidens possesses a non-sucrose-inducible patatin gene. PUBMED:7808402 EPMC:7808402

  2. Mignery GA, Pikaard CS, Park WD; , Gene 1988;62:27-44.: Molecular characterization of the patatin multigene family of potato. PUBMED:3371664 EPMC:3371664


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002641

This domain is structurally and functionally related to the animal cytosolic phospholipase A2.

This domain is found in the patatin glycoproteins from the total soluble protein in potato tubers [PUBMED:3371664]. Patatin is a storage protein but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids [PUBMED:3371664].

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 Patatin (CL0323), which contains the following 3 members:

Acyl_transf_1 Patatin PLA2_B

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(116)
Full
(10726)
Representative proteomes NCBI
(8861)
Meta
(1395)
RP15
(1192)
RP35
(2259)
RP55
(3131)
RP75
(3812)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(116)
Full
(10726)
Representative proteomes NCBI
(8861)
Meta
(1395)
RP15
(1192)
RP35
(2259)
RP55
(3131)
RP75
(3812)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(116)
Full
(10726)
Representative proteomes NCBI
(8861)
Meta
(1395)
RP15
(1192)
RP35
(2259)
RP55
(3131)
RP75
(3812)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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 View help on the curation process

Seed source: Pfam-B_2206 (release 4.1)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A, Dlakic M
Number in seed: 116
Number in full: 10726
Average length of the domain: 181.80 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 39.60 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.4 25.4
Trusted cut-off 25.4 25.4
Noise cut-off 25.3 25.3
Model length: 204
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Structures

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 Patatin domain has been found. There are 5 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.

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