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19  structures 873  species 3  interactions 2796  sequences 109  architectures

Family: DUSP (PF06337)

Summary: DUSP domain

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

This is the Wikipedia entry entitled "Deubiquitinating enzyme". More...

Deubiquitinating enzyme Edit Wikipedia article

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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.

DUSP domain Provide feedback

The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved [1]. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet [1].

Literature references

  1. de Jong RN, Ab E, Diercks T, Truffault V, Daniels M, Kaptein R, Folkers GE;, J Biol Chem. 2006;281:5026-5031.: Solution structure of the human ubiquitin-specific protease 15 DUSP domain. PUBMED:16298993 EPMC:16298993


This tab holds annotation information from the InterPro database.

InterPro entry IPR006615

Deubiquitinating enzymes (DUB) form a large family of cysteine protease that can deconjugate ubiquitin or ubiquitin-like proteins (see PROSITEDOC) from ubiquitin-conjugated proteins. All DUBs contain a catalytic domain surrounded by one or more subdomains, some of which contribute to target recognition. The ~120-residue DUSP (domain present in ubiquitin-specific proteases) domain is one of these specific subdomains. Single or tandem DUSP domains are located both N- and C-terminal to the ubiquitin carboxyl-terminal hydrolase catalytic core domain (see PROSITEDOC) [PUBMED:16298993].

The DUSP domain displays a tripod-like AB3 fold with a three-helix bundle and a three-stranded anti-parallel beta-sheet resembling the legs and seat of the tripod. Conserved residues are predominantly involved in hydrophobic packing interactions within the three alpha-helices. The most conserved DUSP residues, forming the PGPI motif, are flanked by two long loops that vary both in length and sequence. The PGPI motif packs against the three-helix bundle and is highly ordered [PUBMED:16298993].

The function of the DUSP domain is unknown but it may play a role in protein/protein interaction or substrate recognition. This domain is associated with ubiquitin carboxyl-terminal hydrolase family 2 (INTERPRO, MEROPS peptidase family C19). They are a family 100 to 200 kDa peptides which includes the Ubp1 ubiquitin peptidase from yeast; others include:

  • Mammalian ubiquitin carboxyl-terminal hydrolase 4 (USP4),
  • Mammalian ubiquitin carboxyl-terminal hydrolase 11 (USP11),
  • Mammalian ubiquitin carboxyl-terminal hydrolase 15 (USP15),
  • Mammalian ubiquitin carboxyl-terminal hydrolase 20 (USP20),
  • Mammalian ubiquitin carboxyl-terminal hydrolase 32 (USP32),
  • Vertebrate ubiquitin carboxyl-terminal hydrolase 33 (USP33),
  • Vertebrate ubiquitin carboxyl-terminal hydrolase 48 (USP48).

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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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 (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...

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
(134)
Full
(2796)
Representative proteomes UniProt
(4113)
NCBI
(6742)
Meta
(3)
RP15
(734)
RP35
(1420)
RP55
(2080)
RP75
(2502)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(134)
Full
(2796)
Representative proteomes UniProt
(4113)
NCBI
(6742)
Meta
(3)
RP15
(734)
RP35
(1420)
RP55
(2080)
RP75
(2502)
Alignment:
Format:
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Sequence:
Gaps:
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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
(134)
Full
(2796)
Representative proteomes UniProt
(4113)
NCBI
(6742)
Meta
(3)
RP15
(734)
RP35
(1420)
RP55
(2080)
RP75
(2502)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: ADDA_8548
Previous IDs: DUF1055;
Type: Domain
Sequence Ontology: SO:0000417
Author: Yeats C , Bateman A
Number in seed: 134
Number in full: 2796
Average length of the domain: 99.30 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 10.56 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.1 29.1
Trusted cut-off 29.1 29.1
Noise cut-off 29.0 29.0
Model length: 92
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Interactions

There are 3 interactions for this family. More...

Ubiquitin_3 DUSP Ubiquitin_3

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 DUSP domain has been found. There are 19 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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