Summary: WW domain binding protein 11
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WBP11 Edit Wikipedia article
|, NPWBP, PPP1R165, SIPP1, WBP-11, WW domain binding protein 11|
|View/Edit Human||View/Edit Mouse|
- WW domain binding protein 11 (WBP11)
- Npw38-binding protein (NpwBP)
- Splicing factor that Interacts with PQBP-1 and PP1 (SIPP1)
- SH3 domain binding Protein, 70 kDa (SNP70)
Studies suggest that Wbp11 plays a role in DNA/ RNA transcriptional or post-transcriptional events related to cell division. Wbp11 is found in the nucleus but not the nucleoli of cells in interphase. However it is distributed throughout the cytoplasm in dividing cells. Immunoelectron-microscopy experiments suggest that relocation from a peri-nuclear to a cytoplasmic distribution, coinciding with the onset of mitosis in cell division. Other studies have shown that Wbp11 is a component of the spliceosome. Also, that Wbp11 fragments block pre-mRNA splicing catalysis.
Wbp11 is a polypeptide known to interact with other WW domain of proteins such as the nuclear protein Npw38 via two proline-rich regions. It associates with Npw38 (hence the name NpwBP) in the nuclei and with Poly(rG) and G-rich ssDNA. The 70kDa protein has also been found to interact with SH3 (Src homology domain 3) domains. The C-terminal proline-rich sequences of SNP70/NpwBP/Wbp11, which binds to the WW domain of Npw38 also fits with both classic type I and type II SH3 binding sequences, hence the name (SNP70).
Wbp11 was found to bind strongly to the tandem SH3 domains of p47phox and to the N-terminal SH3 domain of p47phox, and more weakly to the SH3 domains from c-src and p85α. p47phox.
Furthermore, it has been shown to interact with PP1(protein phosphotase 1), hence the name SIPP1. It has an inhibitory effect to PP1, with its inhibitory potency increasing upon phosphorylation with protein kinase CK1. The binding of Wbp11 with PP1 involves a RVXF (Arg-Val-Xaa-Phe) motif, which functions as a PP1- binding sequence in most interactors of PP1.
A number of other interactions have been indicated such as:
- Vimentin 
- Growth factor receptor-bound protein 2 (GRB2) 
- Genome polyprotein 
- Tyrosine-protein kinase Fyn 
- Pre-mRNA-processing factor 39 (PRP39) 
- TNF receptor-associated factor 4 (TRAF4) 
- Calcineurin B homologous protein 3 (TESC) 
- Probable ATP-dependent RNA helicase DDX17 
- CD2 antigen cytoplasmic tail-binding protein 2 (CD2BP2) 
- Poly(rC)-binding protein 1 (PCBP1) 
- "Human PubMed Reference:".
- "Mouse PubMed Reference:".
- Komuro A, Saeki M, Kato S (December 1999). "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". The Journal of Biological Chemistry. 274 (51): 36513–9. doi:10.1074/jbc.274.51.36513. PMID 10593949.
- Craggs G, Finan PM, Lawson D, Wingfield J, Perera T, Gadher S, Totty NF, Kellie S (August 2001). "A nuclear SH3 domain-binding protein that colocalizes with mRNA splicing factors and intermediate filament-containing perinuclear networks". The Journal of Biological Chemistry. 276 (32): 30552–60. doi:10.1074/jbc.M103142200. PMID 11375989.
- Llorian M, Beullens M, Andrés I, Ortiz JM, Bollen M (February 2004). "SIPP1, a novel pre-mRNA splicing factor and interactor of protein phosphatase-1". The Biochemical Journal. 378 (Pt 1): 229–38. doi:10.1042/BJ20030950. PMC . PMID 14640981.
- Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, et al. (November 2014). "A proteome-scale map of the human interactome network". Cell. 159 (5): 1212–26. doi:10.1016/j.cell.2014.10.050. PMC . PMID 25416956.
- Dolan PT, Zhang C, Khadka S, Arumugaswami V, Vangeloff AD, Heaton NS, Sahasrabudhe S, Randall G, Sun R, LaCount DJ (December 2013). "Identification and comparative analysis of hepatitis C virus-host cell protein interactions". Molecular bioSystems. 9 (12): 3199–209. doi:10.1039/c3mb70343f. PMC . PMID 24136289.
- Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, et al. (April 2016). "An inter-species protein-protein interaction network across vast evolutionary distance". Molecular Systems Biology. 12 (4): 865. doi:10.15252/msb.20156484. PMC . PMID 27107014.
- Hegele A, Kamburov A, Grossmann A, Sourlis C, Wowro S, Weimann M, Will CL, Pena V, Lührmann R, Stelzl U (February 2012). "Dynamic protein-protein interaction wiring of the human spliceosome". Molecular Cell. 45 (4): 567–80. doi:10.1016/j.molcel.2011.12.034. PMID 22365833.
- Kofler M, Motzny K, Beyermann M, Freund C (September 2005). "Novel interaction partners of the CD2BP2-GYF domain". The Journal of Biological Chemistry. 280 (39): 33397–402. doi:10.1074/jbc.M503989200. PMID 16000308.
- Lim J, Hao T, Shaw C, Patel AJ, Szabó G, Rual JF, Fisk CJ, Li N, Smolyar A, Hill DE, Barabási AL, Vidal M, Zoghbi HY (May 2006). "A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration". Cell. 125 (4): 801–14. doi:10.1016/j.cell.2006.03.032. PMID 16713569.
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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.
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
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.
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)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
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You can see the alignments as HTML or in three different sequence viewers:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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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.
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|Seed source:||Pfam-B_13108 (release 21.0)|
|Author:||Mistry J , Wood V|
|Number in seed:||96|
|Number in full:||963|
|Average length of the domain:||78.90 aa|
|Average identity of full alignment:||35 %|
|Average coverage of the sequence by the domain:||18.54 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the 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:
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".
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.
The tree shows the occurrence of this domain across different species. More...
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.
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:
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