Summary: DUSP domain

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Wikipedia: Deubiquitinating enzyme
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Deubiquitinating enzyme Edit Wikipedia article

Deubiquitinating enzymes (DUBs) are a large group of proteases^[1] (more than 60 known) that regulate ubiquitin-dependent metabolic pathways by cleaving ubiquitin-protein bonds. DUBs are also commonly referred to as deubiquitinating peptidases, deubiquitinating isopeptidases, deubiquitinases, ubiquitin proteases, ubiquitin hydrolyases, ubiquitin isopeptidases, or DUbs. The human genome encodes nearly 100 DUBs with specificity for ubiquitin in five gene families.^[2] Potentially, DUBs may act as negative and positive regulators of the ubiquitin system. In addition to ubiquitin recycling, they are involved in processing of ubiquitin precursors, in proofreading of protein ubiquitination and in disassembly of inhibitory ubiquitin chains.

They may be associated with disease.^[3]

[edit] Classes

DUBs can be classified into two main classes: cysteine proteases and metalloproteases.

[edit] Cysteine proteases

There are four main superfamilies of cysteine protease DUBs:

the ubiquitin-specific processing protease (USP/UBP) superfamily; (USP1, USP2, USP3, USP4, USP5, USP6, USP7, USP8, USP9X, USP9Y, USP10, USP11, USP12, USP13, USP14, USP15, USP16, USP17, USP17L2, USP17L3, USP17L4, USP17L5, USP17L7, USP17L8, USP18, USP19, USP20, USP21, USP22, USP23, USP24, USP25, USP26, USP27X, USP28, USP29, USP30, USP31, USP32, USP33, USP34, USP35, USP36, USP37, USP38, USP39, USP40, USP41, USP42, USP43, USP44, USP45, USP46)
the ovarian tumour (OTU) superfamily;
and the Machado-Josephin domain (MJD) superfamily. (OTUB1, OTUB2, ATXN3, ATXN3L)
the ubiquitin C-terminal hydrolyase (UCH) superfamily; (BAP1, UCHL1, UCHL3, UCHL5)

UCH

usp2 in complex with ubiquitin

Identifiers

Symbol

UCH

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

In molecular biology, Ubiquitin carboxyl-terminal hydrolase (UCH)is a protein which removes a signal compound called, Ubiquitin, from other proteins. These are deubiquitinating enzymes, which means that they remove Ubiquitin from a protein. To date, four members have been known in UCH family: UCH-L1, UCH-L3,UCH37, and BRCA1-associated protein-1 (BAP1), and these all have a conserved catalytic domain (UCH-domain) consisting of about 230 amino acids. UCHs are very important as UCH-L1 levels are high in various types of malignancies (cancer).^[4]

[edit] Function involved with Ubiquitin

Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly.^[5] Since UCH is an de-ubiquitinating enzyme, it removes ubiquitin from a protein and therefore the protein cannot undergo the processes named above.

[edit] Structure

Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative of the cysteine/histidine spacing of a cysteine protease catalytic dyad.^[5]

However, there is also a little known putative group of DUBs called the permutated papain fold peptidases of dsDNA viruses and eukaryote (PPPDEs) superfamily, which, if shown to be bona fide DUBs, would be the fifth in the cysteine protease class.^[6]

[edit] Metalloproteases

The Jab1/Mov34/Mpr1 Pad1 N-terminal+ (MPN+) (JAMM) domain superfamily proteins bind zinc and hence are metalloproteases.

[edit] Role in the ubiquitin pathway

DUBs play several roles in the ubiquitin pathway. First, DUBs carry out activation of the ubiquitin proproteins, probably cotranslationally. Second, DUBs recycle ubiquitin that may have been accidentally trapped by the reaction of small cellular nucleophiles with the thiol ester intermediates involved in the ubiquitination of proteins. Third, DUBs reverse the ubiquitination or ubiquitin-like modification of target proteins. Fourth, DUBs are also responsible for the regeneration of monoubiquitin from unanchored polyubiquitin, i.e., free polyubiquitin that is synthesized de novo by the conjugating machinery or that has been released from target proteins by other DUBs.^[2] Finally, the deubiquitinating enzymes UCH-L3 and YUH1 are able to hydrolyse mutant ubiquitin UBB+1 despite of the fact that the glycine at position 76 is mutated.^[7]

[edit] Domain architecture

DUSP domain

solution structure of the dusp domain of husp15

Identifiers

Symbol

DUSP

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

All DUBs contain a catalytic domain surrounded by one or more subdomains, some of which contribute to target recognition. The ~120-residue DUSP (domain present in ubiquitin-specific proteases) domain is one of these specific subdomains. Single or tandem DUSP domains are located both N- and C-terminal to the ubiquitin carboxyl-terminal hydrolase catalytic core domain.^[8] The DUSP domain displays a tripod-like AB3 fold with a three-helix bundle and a three-stranded anti-parallel beta-sheet resembling the legs and seat of the tripod. Conserved residues are predominantly involved in hydrophobic packing interactions within the three alpha-helices. The most conserved DUSP residues, forming the PGPI motif, are flanked by two long loops that vary both in length and sequence. The PGPI motif packs against the three-helix bundle and is highly ordered.^[8] The function of the DUSP domain is unknown but it may play a role in protein/protein interaction or substrate recognition.

[edit] References

^ Wilkinson K (1997). "Regulation of ubiquitin-dependent processes by deubiquitinating enzymes". FASEB J. 11 (14): 1245–56. PMID 9409543.
^ ^a ^b Reyes Turcu FE, Ventii KH, Wilkinson KD (2009). "Activity and Cellular Roles of Ubiquitin-Specific Deubiquitinating Enzymes". Annual Review of Biochemistry 78: 363–97. doi:10.1146/annurev.biochem.78.082307.091526. PMC 2734102. PMID 19489724. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2734102/.
^ Singhal S, Taylor MC, Baker RT (2008). "Deubiquitylating enzymes and disease". BMC Biochem. 9 Suppl 1: S3. doi:10.1186/1471-2091-9-S1-S3. PMC 2582804. PMID 19007433. http://www.biomedcentral.com/1471-2091/9%20Suppl%201/S3.
^ Fang Y, Fu D, Shen XZ (2010). "The potential role of ubiquitin c-terminal hydrolases in oncogenesis.". Biochim Biophys Acta 1806 (1): 1–6. doi:10.1016/j.bbcan.2010.03.001. PMID 20302916. http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=20302916.
^ ^a ^b Rawlings ND, Barrett AJ (1994). "Families of cysteine peptidases". Meth. Enzymol. 244: 461–86. doi:10.1016/0076-6879(94)44034-4. PMID 7845226.
^ Iyer LM, Koonin EV, Aravind L (2004). "Novel predicted peptidases with a potential role in the ubiquitin signaling system". Cell Cycle 3 (11): 1440–50. doi:10.4161/cc.3.11.1206. PMID 15483401.
^ Dennissen, F; Kholod N, Hermes DJ, Kemmerling N, Steinbusch HW, Dantuma NP, van Leeuwen FW. (6 July 2011). "Mutant ubiquitin (UBB(+1)) associated with neurodegenerative disorders is hydrolyzed by ubiquitin C-terminal hydrolase L3 (UCH-L3).". FEBSletters 585 (16): 2568–74. doi:10.1016/j.febslet.2011.06.037. PMID 21762696. http://www.sciencedirect.com/science/article/pii/S0014579311005138.
^ ^a ^b de Jong RN, Ab E, Diercks T, Truffault V, Daniels M, Kaptein R, Folkers GE (February 2006). "Solution structure of the human ubiquitin-specific protease 15 DUSP domain". J. Biol. Chem. 281 (8): 5026–31. doi:10.1074/jbc.M510993200. PMID 16298993.

Posttranslational modification

Chaperones/
protein folding

Heat shock proteins/ Chaperonins	Hsp10/GroES Early pregnancy factor Hsp27 Hsp47 HSP60/GroEL Hsp40/DnaJ A1 A2 A3 B1 B2 B11 B4 B6 B9 C1 C3 C5 C6 C7 C10 C11 C13 C14 C19 Hsp70 1A 1B 1L 2 4 4L 5 6 7 8 9 12A 14 Hsp90 α₁ α₂ β ER TRAP1

Other	Alpha crystallin Clusterin Survival of motor neuron SMN1 SMN2

Protein targeting

Signal peptide Mitochondrial targeting signal

Ubiquitin

E1 Ubiquitin-activating enzyme
- UBA1
- UBA2
- UBA3
- UBA5
- UBA6
- UBA7
- ATG7
- NAE1
- SAE1

E2 Ubiquitin-conjugating enzyme
- A
- B
- C
- D1
- D2
- D3
- E1
- E2
- E3
- G1
- G2
- H
- I
- J1
- J2
- K
- L1
- L2
- L3
- L4
- L6
- M
- N
- O
- Q1
- Q2
- R1 (CDC34)
- R2
- S
- V1
- V2
- Z

E3 Ubiquitin ligase
- VHL
- Cullin
- CBL
- MDM2
- FANCL
- UBR1

Deubiquitinating enzyme: Ataxin 3
USP6
CYLD

Other

Ubiquitin-like modifiers
- SUMO protein
- ISG15
- URM1
- NEDD8
- FAT10
- ATG8
- ATG12
- FUB1
- MUB
- UFM1
- UBL5

See also: posttranslational modification disorders
B bsyn: dna (repl, cycl, reco, repr) · tscr (fact, tcrg, nucl, rnat, rept, ptts) · tltn (risu, pttl, nexn) · dnab, rnab/runp · stru (domn, 1°, 2°, 3°, 4°)

This article incorporates text from the public domain Pfam and InterPro IPR006615

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.

DUSP domain Provide feedback

The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved [1]. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet [1].

Literature references

de Jong RN, Ab E, Diercks T, Truffault V, Daniels M, Kaptein R, Folkers GE;, J Biol Chem. 2006;281:5026-5031.: Solution structure of the human ubiquitin-specific protease 15 DUSP domain. PUBMED:16298993 EPMC:16298993

External database links

MEROPS:	C19
PANDIT:	PF06337
Pseudofam:	PF06337
SYSTERS:	DUSP

This tab holds annotation information from the InterPro database.

InterPro entry IPR006615

Deubiquitinating enzymes (DUB) form a large family of cysteine protease that can deconjugate ubiquitin or ubiquitin-like proteins (see PROSITEDOC) from ubiquitin-conjugated proteins. All DUBs contain a catalytic domain surrounded by one or more subdomains, some of which contribute to target recognition. The ~120-residue DUSP (domain present in ubiquitin-specific proteases) domain is one of these specific subdomains. Single or tandem DUSP domains are located both N- and C-terminal to the ubiquitin carboxyl-terminal hydrolase catalytic core domain (see PROSITEDOC) [PUBMED:16298993].

The DUSP domain displays a tripod-like AB3 fold with a three-helix bundle and a three-stranded anti-parallel beta-sheet resembling the legs and seat of the tripod. Conserved residues are predominantly involved in hydrophobic packing interactions within the three alpha-helices. The most conserved DUSP residues, forming the PGPI motif, are flanked by two long loops that vary both in length and sequence. The PGPI motif packs against the three-helix bundle and is highly ordered [PUBMED:16298993].

The function of the DUSP domain is unknown but it may play a role in protein/protein interaction or substrate recognition. This domain is associated with ubiquitin carboxyl-terminal hydrolase family 2 (INTERPRO, MEROPS peptidase family C19). They are a family 100 to 200 kDa peptides which includes the Ubp1 ubiquitin peptidase from yeast; others include:

Mammalian ubiquitin carboxyl-terminal hydrolase 4 (USP4),
Mammalian ubiquitin carboxyl-terminal hydrolase 11 (USP11),
Mammalian ubiquitin carboxyl-terminal hydrolase 15 (USP15),
Mammalian ubiquitin carboxyl-terminal hydrolase 20 (USP20),
Mammalian ubiquitin carboxyl-terminal hydrolase 32 (USP32),
Vertebrate ubiquitin carboxyl-terminal hydrolase 33 (USP33),
Vertebrate ubiquitin carboxyl-terminal hydrolase 48 (USP48).

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function

ubiquitin thiolesterase activity (GO:0004221)

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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

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 (139)	Full (806)	Representative proteomes				NCBI (743)	Meta (3)
	Seed (139)	Full (806)	RP15 (219)	RP35 (288)	RP55 (414)	RP75 (544)	NCBI (743)	Meta (3)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (139)	Full (806)	Representative proteomes				NCBI (743)	Meta (3)
	Seed (139)	Full (806)	RP15 (219)	RP35 (288)	RP55 (414)	RP75 (544)	NCBI (743)	Meta (3)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	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 (139)	Full (806)	Representative proteomes				NCBI (743)	Meta (3)
	Seed (139)	Full (806)	RP15 (219)	RP35 (288)	RP55 (414)	RP75 (544)	NCBI (743)	Meta (3)
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

Seed source:

ADDA_8548

Previous IDs:

DUF1055;

Type:

Domain

Author:

Yeats C, Bateman A

Number in seed:

139

Number in full:

806

Average length of the domain:

98.80 aa

Average identity of full alignment:

29 %

Average coverage of the sequence by the domain:

10.54 %

HMM information

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	29.1	29.1
Trusted cut-off	29.2	29.1
Noise cut-off	28.6	29.0

Model length:

99

Family (HMM) version:

7

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Tree controls

Hide

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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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 DUSP domain has been found. There are 12 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.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: DUSP (PF06337)

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