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7  structures 290  species 0  interactions 348  sequences 21  architectures

Family: PFU (PF09070)

Summary: PFU (PLAA family ubiquitin binding)

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

PFU (PLAA family ubiquitin binding) Provide feedback

This domain is found N terminal to PF08324 and binds to ubiquitin [1].

Literature references

  1. Mullally JE, Chernova T, Wilkinson KD; , Mol Cell Biol. 2006;26:822-830.: Doa1 is a Cdc48 adapter that possesses a novel ubiquitin binding domain. PUBMED:16428438 EPMC:16428438


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015155

The PFU (for PLAA family ubiquitin binding domain) is an ubiquitin binding domain with no homology to several known ubiquitin binding domains (e.g., UIM, NZF, UBA, UEV, UBP, or CUE domains). The PFU domain appears to be unique to the PLAA family of proteins. A single member of this family of proteins exists in every eukaryotic species examined. Each of these homologues possesses identical domain structure: an N-terminal domain containing seven WD40 repeats, a central PFU domain, and a C-terminal PUL domain, which directly binds to Cdc48, a member of the AAA-ATPase family of molecular chaperone [PUBMED:16428438]. In addition to ubiquitin, the PFU domain of DOA1 has been shown to bind to the SH3 domain [PUBMED:18508771].

Secondary structure predictions of the PFU domain suggest the presence of an extensive length of beta-sheet, N-terminal to an alpha-helical region [PUBMED:16428438].

Some proteins known to contain a PFU domain include:

  • Saccharomyces cerevisiae DOA1 (UFD3, ZZZ4), involved in the ubiquitin conjugation pathway. DOA1 participates in the regulation of the ubiquitin conjugation pathway involving CDC48 by hindering multiubiquitination of substrates at the CDC48 chaperone.
  • Schizosaccharomyces pombe ubiquitin homeostasis protein Lub1, acts as a negative regulator of vacuole-dependent ubiquitin degradation.
  • Mammalian phospholipase A-2-activating protein (PLA2P, PLAA), the homologue of DOA1. PLA2P plays an important role in the regulation of specific inflammatory disease processes.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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
(39)
Full
(348)
Representative proteomes NCBI
(358)
Meta
(3)
RP15
(91)
RP35
(141)
RP55
(207)
RP75
(246)
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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
(39)
Full
(348)
Representative proteomes NCBI
(358)
Meta
(3)
RP15
(91)
RP35
(141)
RP55
(207)
RP75
(246)
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
(39)
Full
(348)
Representative proteomes NCBI
(358)
Meta
(3)
RP15
(91)
RP35
(141)
RP55
(207)
RP75
(246)
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_5813 (release 20.0)
Previous IDs: none
Type: Domain
Author: Mistry J
Number in seed: 39
Number in full: 348
Average length of the domain: 111.50 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 15.52 %

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 20.9 20.9
Trusted cut-off 21.1 22.1
Noise cut-off 20.8 20.8
Model length: 116
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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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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The tree shows the occurrence of this domain across different species. More...

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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 PFU domain has been found. There are 7 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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