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15  structures 279  species 1  interaction 2346  sequences 72  architectures

Family: UIM (PF02809)

Summary: Ubiquitin interaction motif

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 "Ubiquitin interacting motif". More...

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Ubiquitin interaction motif Provide feedback

This motif is called the ubiquitin interaction motif. One of the proteins containing this motif is a receptor for poly-ubiquitination chains for the proteasome [1]. This motif has a pattern of conservation characteristic of an alpha helix.

Literature references

  1. Hiyama H, Yokoi M, Masutani C, Sugasawa K, Maekawa T, Tanaka K, Hoeijmakers JH, Hanaoka F; , J Biol Chem 1999;274:28019-28025.: Interaction of hHR23 with S5a. The ubiquitin-like domain of hHR23 mediates interaction with S5a subunit of 26 S proteasome. PUBMED:10488153 EPMC:10488153


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003903

The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [PUBMED:9488668,PUBMED:11406394]. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains [PUBMED:12062168]. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (INTERPRO), UBX (INTERPRO), ENTH, EH (INTERPRO), VHS (INTERPRO), SH3 (INTERPRO), HECT (INTERPRO), VWFA (INTERPRO), EF-hand calcium-binding, WD-40 (INTERPRO), F-box (INTERPRO), LIM (INTERPRO), protein kinase (INTERPRO), ankyrin (INTERPRO), PX (INTERPRO), phosphatidylinositol 3- and 4-kinase (INTERPRO), C2 (INTERPRO), OTU (INTERPRO), dnaJ (INTERPRO), RING-finger (INTERPRO) or FYVE-finger (INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [PUBMED:12121618, PUBMED:11919614, PUBMED:1919637].

The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds [PUBMED:11406394]. Some proteins known to contain an UIM are listed below:

  • Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome.
  • Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD).
  • Vertebrate epsin and epsin2.
  • Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS).
  • Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation.
  • Mammalian epidermal growth factor receptor substrate EPS15R.
  • Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin.
  • Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole.

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...

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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
(46)
Full
(2346)
Representative proteomes NCBI
(2205)
Meta
(32)
RP15
(264)
RP35
(430)
RP55
(695)
RP75
(978)
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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
(46)
Full
(2346)
Representative proteomes NCBI
(2205)
Meta
(32)
RP15
(264)
RP35
(430)
RP55
(695)
RP75
(978)
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
(46)
Full
(2346)
Representative proteomes NCBI
(2205)
Meta
(32)
RP15
(264)
RP35
(430)
RP55
(695)
RP75
(978)
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.

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: Aravind L
Previous IDs: none
Type: Motif
Author: Aravind L
Number in seed: 46
Number in full: 2346
Average length of the domain: 17.30 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 7.58 %

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 20.4 2.9
Trusted cut-off 20.4 4.0
Noise cut-off 20.3 -1000000.0
Model length: 18
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

ubiquitin

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 UIM domain has been found. There are 15 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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