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24  structures 1302  species 0  interactions 10588  sequences 228  architectures

Family: UIM (PF02809)

Summary: Ubiquitin interaction motif

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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

Internal database links

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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Pfam Clan

This family is a member of clan UIM (CL0702), which has the following description:

This clan includes families containing the ubiquitin interacting motif (UIM) involved in the recognition of polyUb chains which forms an alpha-helix with an unexpected hairpin loop that contributes to the binding interface with Ubl. Families in this clan have one or more UIM motifs, providing different binding properties or targets and a wide range of functions.

The clan contains the following 2 members:



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

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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...


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Curation and family details

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Seed source: Aravind L
Previous IDs: none
Type: Motif
Sequence Ontology: SO:0001067
Author: Aravind L
Number in seed: 113
Number in full: 10588
Average length of the domain: 16.50 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 5.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 2.9
Trusted cut-off 21.0 6.1
Noise cut-off 20.9 -1000000.0
Model length: 17
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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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 24 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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