Summary

Ubiquitin family

This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Q02724), Nedd8 (see P29595), Elongin B (see Q15370), Rub1 (see Q9SHE7), and Parkin (see O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].

Literature references

Vijay-Kumar S, Bugg CE, Cook WJ; , J Mol Biol 1987;194:531-544.: Structure of ubiquitin refined at 1.8 A resolution. PUBMED:3041007
Cook WJ, Jeffrey LC, Kasperek E, Pickart CM; , J Mol Biol 1994;236:601-609.: Structure of tetraubiquitin shows how multiubiquitin chains can be formed. PUBMED:8107144
Bayer P, Arndt A, Metzger S, Mahajan R, Melchior F, Jaenicke R, Becker J; , J Mol Biol 1998;280:275-286.: Structure determination of the small ubiquitin-related modifier SUMO-1. PUBMED:9654451
Whitby FG, Xia G, Pickart CM, Hill CP; , J Biol Chem 1998;273:34983-34991.: Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes. PUBMED:9857030
Upadhya SC, Hegde AN; , Trends Biochem Sci 2003;28:280-283.: A potential proteasome-interacting motif within the ubiquitin-like domain of parkin and other proteins. PUBMED:12826399

InterPro entry IPR000626

Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, ), a ubiquitin-conjugating enzyme (E2, ), and a ubiquitin ligase (E3, , ), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process PUBMED:12646216. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (), SUMO1 (), NEDD8, Rad23 (), Elongin B and Parkin (), the latter being involved in Parkinson's disease PUBMED:15564047.

Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome PUBMED:15454246. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking PUBMED:14998368. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation PUBMED:15556404. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation PUBMED:15525528.

Clan

This family is a member of clan Ubiquitin (CL0072), which contains the following 25 members:

APG12 CIDE-N DUF1017 DUF1315 DWNN FERM_N MAP1_LC3 NQRA_SLBB PB1 PI3K_rbd RA Rad60-SLD RBD SLBB TGS ThiS TUG ubiquitin UBX Ufm1 UN_NPL4 UPF0125 Urm1 YchF-GTPase_C YukD

External database links

HOMSTRAD:	UBQ
PANDIT:	PF00240
PRINTS:	PR00348
PROSITE:	PDOC00271
SCOP:	1aar
SYSTERS:	ubiquitin

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

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Alignment:	Seed (78) Full (5947) NCBI (11321) Metagenomics (374)
Viewer:

Formatting options

Alignment:	Seed (78) Full (5947)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

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

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (78) Full (5947) NCBI (11321) Metagenomics (374)
Full length sequences	Full-sequences (5947)

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 HMMER2.

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. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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

Seed source:

Prosite

Previous IDs:

none

Type:

Domain

Author:

Finn RD, Griffiths-Jones SR

Number in seed:

78

Number in full:

5947

Average length of the domain:

67.00 aa

Average identity of full alignment:

48 %

Average coverage of the sequence by the domain:

18.83 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.7	20.7
Trusted cut-off	20.7	20.7
Noise cut-off	20.6	20.6

Model length:

69

Family (HMM) version:

16

Download:

download the raw HMM for this family

Species distribution

Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Interactions

There are 16 interactions for this family. More...

UBACT zf-UBP UIM CUE Peptidase_C48 UDG UBA_e1_thiolCys Vps36_ESCRT-II UBA ThiF Peptidase_C12 zf-A20 ubiquitin UQ_con SH3_1 UCH

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 ubiquitin domain has been found.

Loading structure mapping...

Family: ubiquitin (PF00240)

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