Summary: Ubiquitin interaction motif
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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 . This motif has a pattern of conservation characteristic of an alpha helix.
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
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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.
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Curation and family details
|Seed source:||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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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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