Summary: WW domain binding protein 11

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Wikipedia: WBP11
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WBP11 Edit Wikipedia article

Wbp11

Identifiers

Symbol

Wbp11

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

WW domain binding protein 11

Identifiers

Symbols

WBP11; NPWBP; SIPP1; WBP-11

External IDs

MGI: 1891823 HomoloGene: 9466 GeneCards: WBP11 Gene

Gene Ontology
Molecular function	â¢ single-stranded DNA binding â¢ protein binding â¢ protein phosphatase type 1 regulator activity â¢ WW domain binding
Cellular component	â¢ nucleus â¢ cytoplasm â¢ nuclear speck
Biological process	â¢ rRNA processing â¢ mRNA processing â¢ RNA splicing
Sources: Amigo / QuickGO

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 12:
14.94 â 14.96 Mb

Chr 6:
136.81 â 136.83 Mb

PubMed search

[1]

[2]

[edit] Alternative Names

WW domain binding protein 11 (WBP1)
Rsp5
WWP domain

[edit] Function

WW domain-binding protein 11 is a protein that in humans, is encoded by the WBP11 gene. The function of WBP11 is to play a role in the regulation of pre-mRNA processing. More specifically, this nuclear protein, colocalizes with mRNA splicing factors and intermediate filament-containing perinuclear networks.^[1]^[2]

[edit] Structure

The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins.^[3]^[4]^[5]^[6] The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Proline. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs.^[7]^[8] It is frequently associated with other domains typical for proteins in signal transduction processes.

[edit] Protein interactions

Wbp11 contains two proline-rich regions that bind to the WW domain of the nuclear protein, Npw38, hence leading to its alternative name, Npw38-binding protein, NpwBP. The Npw38-NpwBP complex functions as a component of an mRNA factory in the nucleus.^[2] WBP11 has also been shown to interact with PQBP1.^[1]^[9]

[edit] Proteins containing Wbp11 domain

A large variety of proteins containing the WW domain are known. These include:

dystrophin, a multidomain cytoskeletal protein;
utrophin, a dystrophin-like protein of unknown function;
vertebrate YAP protein, substrate of an unknown serine kinase;
Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system;
Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation;
Rattus norvegicus (Rat) FE65, a transcription factor activator expressed preferentially in liver;
Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.

[edit] References

^ ^a ^b Komuro A, Saeki M, Kato S (January 2000). "Association of two nuclear proteins, Npw38 and NpwBP, via the interaction between the WW domain and a novel proline-rich motif containing glycine and arginine". J Biol Chem 274 (51): 36513â9. doi:10.1074/jbc.274.51.36513. PMID 10593949.
^ ^a ^b "Entrez Gene: WBP11 WW domain binding protein 11".
^ Bork P, Sudol M (December 1994). "The WW domain: a signalling site in dystrophin?". Trends Biochem. Sci. 19 (12): 531â3. doi:10.1016/0968-0004(94)90053-1. PMID 7846762.
^ AndrÃÂ© B, Springael JY (December 1994). "WWP, a new amino acid motif present in single or multiple copies in various proteins including dystrophin and the SH3-binding Yes-associated protein YAP65". Biochem. Biophys. Res. Commun. 205 (2): 1201â5. doi:10.1006/bbrc.1994.2793. PMID 7802651.
^ Hofmann K, Bucher P (January 1995). "The rsp5-domain is shared by proteins of diverse functions". FEBS Lett. 358 (2): 153â7. doi:10.1016/0014-5793(94)01415-W. PMID 7828727.
^ Sudol M, Chen HI, Bougeret C, Einbond A, Bork P (August 1995). "Characterization of a novel protein-binding module--the WW domain". FEBS Lett. 369 (1): 67â71. doi:10.1016/0014-5793(95)00550-S. PMID 7641887.
^ Chen HI, Sudol M (August 1995). "The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules". Proc. Natl. Acad. Sci. U.S.A. 92 (17): 7819â23. doi:10.1073/pnas.92.17.7819. PMC 41237. PMID 7644498.
^ Macias MJ, Wiesner S, Sudol M (February 2002). "WW and SH3 domains, two different scaffolds to recognize proline-rich ligands". FEBS Lett. 513 (1): 30â7. doi:10.1016/S0014-5793(01)03290-2. PMID 11911877.
^ Zhang, Y; Lindblom T, Chang A, Sudol M, Sluder A E, Golemis E A (October 2000). "Evidence that dim1 associates with proteins involved in pre-mRNA splicing, and delineation of residues essential for dim1 interactions with hnRNP F and Npw38/PQBP-1". Gene (NETHERLANDS) 257 (1): 33â43. doi:10.1016/S0378-1119(00)00372-3. ISSN 0378-1119. PMID 11054566.

This article incorporates text from the public domain Pfam and InterPro IPR019007

[edit] Further reading

Bedford MT, Sarbassova D, Xu J, et al. (2000). "A novel pro-Arg motif recognized by WW domains.". J. Biol. Chem. 275 (14): 10359â69. doi:10.1074/jbc.275.14.10359. PMID 10744724.
Craggs G, Finan PM, Lawson D, et al. (2001). "A nuclear SH3 domain-binding protein that colocalizes with mRNA splicing factors and intermediate filament-containing perinuclear networks.". J. Biol. Chem. 276 (32): 30552â60. doi:10.1074/jbc.M103142200. PMID 11375989.
Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899â903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
Llorian M, Beullens M, AndrÃ©s I, et al. (2004). "SIPP1, a novel pre-mRNA splicing factor and interactor of protein phosphatase-1.". Biochem. J. 378 (Pt 1): 229â38. doi:10.1042/BJ20030950. PMC 1223944. PMID 14640981.
Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).". Genome Res. 14 (10B): 2121â7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.
Andersen JS, Lam YW, Leung AK, et al. (2005). "Nucleolar proteome dynamics.". Nature 433 (7021): 77â83. doi:10.1038/nature03207. PMID 15635413.
Llorian M, Beullens M, Lesage B, et al. (2006). "Nucleocytoplasmic shuttling of the splicing factor SIPP1.". J. Biol. Chem. 280 (46): 38862â9. doi:10.1074/jbc.M509185200. PMID 16162498.
Rual JF, Venkatesan K, Hao T, et al. (2005). "Towards a proteome-scale map of the human protein-protein interaction network.". Nature 437 (7062): 1173â8. doi:10.1038/nature04209. PMID 16189514.
Lim J, Hao T, Shaw C, et al. (2006). "A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration.". Cell 125 (4): 801â14. doi:10.1016/j.cell.2006.03.032. PMID 16713569.
Olsen JV, Blagoev B, Gnad F, et al. (2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.". Cell 127 (3): 635â48. doi:10.1016/j.cell.2006.09.026. PMID 17081983.

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WW domain binding protein 11 Provide feedback

The WW domain is a small protein module with a triple-stranded beta-sheet fold. This is a family of WW domain binding proteins.

Literature references

Komuro A, Saeki M, Kato S;, J Biol Chem. 1999;274:36513-36519.: Association of two nuclear proteins, Npw38 and NpwBP, via the interaction between the WW domain and a novel proline-rich motif containing glycine and arginine. PUBMED:10593949 EPMC:10593949

External database links

PANDIT:	PF09429
Pseudofam:	PF09429
SYSTERS:	Wbp11

This tab holds annotation information from the InterPro database.

InterPro entry IPR019007

Synonym(s): Rsp5 or WWP domain

The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [PUBMED:7846762, PUBMED:7802651, PUBMED:7828727, PUBMED:7641887]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [PUBMED:7644498, PUBMED:11911877]. It is frequently associated with other domains typical for proteins in signal transduction processes.

A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.

This entry represents WW domain-binding protein 11, which may play a role in the regulation of pre-mRNA processing.

Gene Ontology

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

Biological process

RNA processing (GO:0006396)

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 (30)	Full (272)	Representative proteomes				NCBI (259)	Meta (1)
	Seed (30)	Full (272)	RP15 (63)	RP35 (99)	RP55 (149)	RP75 (198)	NCBI (259)	Meta (1)
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 (30)	Full (272)	Representative proteomes				NCBI (259)	Meta (1)
	Seed (30)	Full (272)	RP15 (63)	RP35 (99)	RP55 (149)	RP75 (198)	NCBI (259)	Meta (1)
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 (30)	Full (272)	Representative proteomes				NCBI (259)	Meta (1)
	Seed (30)	Full (272)	RP15 (63)	RP35 (99)	RP55 (149)	RP75 (198)	NCBI (259)	Meta (1)
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:

Pfam-B_13108 (release 21.0)

Previous IDs:

none

Type:

Family

Author:

Mistry J, Wood V

Number in seed:

30

Number in full:

272

Average length of the domain:

77.90 aa

Average identity of full alignment:

41 %

Average coverage of the sequence by the domain:

17.48 %

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	21.1	21.1
Trusted cut-off	21.7	21.7
Noise cut-off	20.7	20.7

Model length:

78

Family (HMM) version:

5

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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Wbp11 (PF09429)

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