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24  structures 1394  species 0  interactions 12520  sequences 237  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...

Ubiquitin-interacting motif Edit Wikipedia article

UIM
PDB 1yx5 EBI.jpg
solution structure of s5a uim-1/ubiquitin complex
Identifiers
SymbolUIM
PfamPF02809
InterProIPR003903
SCOP21p9d / SCOPe / SUPFAM

In molecular biology, the Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a sequence motif of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin.[1][2] 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.[3] 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.[4][5][6]

The UIM is unlikely to form an independent protein 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.[2] Some proteins known to contain an UIM are listed below:

References

  1. ^ Young P, Deveraux Q, Beal RE, Pickart CM, Rechsteiner M (1998). "Characterization of two polyubiquitin binding sites in the 26 S protease subunit 5a". J. Biol. Chem. 273 (10): 5461–7. PMID 9488668. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ a b Hofmann K, Falquet L (2001). "A ubiquitin-interacting motif conserved in components of the proteasomal and lysosomal protein degradation systems". Trends Biochem. Sci. 26 (6): 347–50. PMID 11406394. {{cite journal}}: Unknown parameter |month= ignored (help)
  3. ^ Buchberger A (2002). "From UBA to UBX: new words in the ubiquitin vocabulary". Trends Cell Biol. 12 (5): 216–21. PMID 12062168. {{cite journal}}: Unknown parameter |month= ignored (help)
  4. ^ Oldham CE, Mohney RP, Miller SL, Hanes RN, O'Bryan JP (2002). "The ubiquitin-interacting motifs target the endocytic adaptor protein epsin for ubiquitination". Curr. Biol. 12 (13): 1112–6. PMID 12121618. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  5. ^ Riezman H (2002). "Cell biology: the ubiquitin connection". Nature. 416 (6879): 381–3. doi:10.1038/416381a. PMID 11919614. {{cite journal}}: Unknown parameter |month= ignored (help)
  6. ^ Reece DE, Barnett MJ, Connors JM, Fairey RN, Fay JW, Greer JP, Herzig GP, Herzig RH, Klingemann HG, LeMaistre CF (1991). "Intensive chemotherapy with cyclophosphamide, carmustine, and etoposide followed by autologous bone marrow transplantation for relapsed Hodgkin's disease". J. Clin. Oncol. 9 (10): 1871–9. PMID 1919637. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR003903

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This is the Wikipedia entry entitled "Ubiquitin interacting motif". More...

Ubiquitin interacting motif Edit Wikipedia article

  • From a page move: This is a redirect from a page that has been moved (renamed). This page was kept as a redirect to avoid breaking links, both internal and external, that may have been made to the old page name.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

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:

RAP80_UIM UIM

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 and the UniProtKB 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
(112)
Full
(12520)
Representative proteomes UniProt
(21714)
RP15
(1769)
RP35
(4579)
RP55
(9284)
RP75
(13263)
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PP/heatmap 1            

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

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

Format an alignment

  Seed
(112)
Full
(12520)
Representative proteomes UniProt
(21714)
RP15
(1769)
RP35
(4579)
RP55
(9284)
RP75
(13263)
Alignment:
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Sequence:
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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
(112)
Full
(12520)
Representative proteomes UniProt
(21714)
RP15
(1769)
RP35
(4579)
RP55
(9284)
RP75
(13263)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Aravind L
Previous IDs: none
Type: Motif
Sequence Ontology: SO:0001067
Author: Aravind L
Number in seed: 112
Number in full: 12520
Average length of the domain: 16.5 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 5.96 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 2.9
Trusted cut-off 21.0 6.3
Noise cut-off 20.9 -1000000.0
Model length: 17
Family (HMM) version: 23
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

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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 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044S174 View 3D Structure Click here
A0A0D2FZX2 View 3D Structure Click here
A0A0D2H034 View 3D Structure Click here
A0A0K0DS66 View 3D Structure Click here
A0A0K0J2P8 View 3D Structure Click here
A0A0N4U972 View 3D Structure Click here
A0A0R0GAE0 View 3D Structure Click here
A0A0R4ITP2 View 3D Structure Click here
A0A150ASP6 View 3D Structure Click here
A0A175WDN7 View 3D Structure Click here
A0A1C1CJ76 View 3D Structure Click here
A0A1D6JVQ5 View 3D Structure Click here
A0A1D6PF20 View 3D Structure Click here
A0A3P7DAU8 View 3D Structure Click here
A1CEK1 View 3D Structure Click here
A1DFP5 View 3D Structure Click here
A2QWA2 View 3D Structure Click here
A3LX75 View 3D Structure Click here
A4HTD8 View 3D Structure Click here
A4QTV1 View 3D Structure Click here
A5PMY5 View 3D Structure Click here
B5DF55 View 3D Structure Click here
C0NHA1 View 3D Structure Click here
C0NS20 View 3D Structure Click here
C1GRW5 View 3D Structure Click here
C1H2L1 View 3D Structure Click here
D4ABE5 View 3D Structure Click here
D4ACD3 View 3D Structure Click here
E1C213 View 3D Structure Click here
E2RK09 View 3D Structure Click here
E7F2A4 View 3D Structure Click here
E7F6T8 View 3D Structure Click here
F1N5V1 View 3D Structure Click here
F1SRY5 View 3D Structure Click here
I1J8K2 View 3D Structure Click here
I1JCF9 View 3D Structure Click here
I1LI24 View 3D Structure Click here
I1MN40 View 3D Structure Click here
J9FA02 View 3D Structure Click here
K7MNT8 View 3D Structure Click here