Summary: TAP C-terminal domain
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|Nuclear RNA export factor 1|
|RNA expression pattern|
This gene is one member of a family of nuclear RNA export factor genes. Common domain features of this family are a noncanonical RNP-type RNA-binding domain (RBD), 4 leucine-rich repeats (LRRs), a nuclear transport factor 2 (NTF2)-like domain that allows heterodimerization with NTF2-related export protein-1 (NXT1), and a ubiquitin-associated domain that mediates interactions with nucleoporins. Alternative splicing results in transcript variants. The LRRs and NTF2-like domains are required for export activity. The encoded protein of this gene shuttles between the nucleus and the cytoplasm and binds in vivo to poly(A)+ RNA. It is the vertebrate homologue of the yeast protein Mex67p. The encoded protein overcomes the mRNA export block caused by the presence of saturating amounts of CTE (constitutive transport element) RNA of type D retroviruses. A variant allele of the homologous Nxf1 gene in mice suppresses a class of mutations caused by integration of an endogenous retrovirus (intracisternal A particle) into an intron.
complex between tap uba domain and fxfg nucleoporin peptide
- vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1).
- Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1).
- yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see <a class="ext" href="http://expasy.org/prosite/PDOC00030">PROSITEDOC</a>) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see <a class="ext" href="http://expasy.org/prosite/PDOC50177">PROSITEDOC</a>) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling.
The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker.
Nuclear export of mRNAs is mediated by the Tap protein.
Tap can form a multimeric complex with itself and with other members of the NXF family. Three functional domains of Tap have been well characterized: the RNA-binding domain, the Nuclear Transport Factor 2 (NTF2)-like domain, and the ubiquitin-associated (UBA) domain.
- Yoon DW, Lee H, Seol W, DeMaria M, Rosenzweig M, Jung JU (May 1997). "Tap: a novel cellular protein that interacts with tip of herpesvirus saimiri and induces lymphocyte aggregation". Immunity 6 (5): 571â82. doi:10.1016/S1074-7613(00)80345-3. PMID 9175835.
- GrÃ¼ter P, Tabernero C, von Kobbe C, et al. (April 1998). "TAP, the human homolog of Mex67p, mediates CTE-dependent RNA export from the nucleus". Mol. Cell 1 (5): 649â59. doi:10.1016/S1097-2765(00)80065-9. PMID 9660949.
- Katahira J, StrÃ¤sser K, Podtelejnikov A, Mann M, Jung JU, Hurt E (May 1999). "The Mex67p-mediated nuclear mRNA export pathway is conserved from yeast to human". EMBO J. 18 (9): 2593â609. doi:10.1093/emboj/18.9.2593. PMC 1171339. PMID 10228171.
- "Entrez Gene: NXF1 nuclear RNA export factor 1".
- Floyd JA, Gold DA, Concepcion D, Poon TH, Wang X, Keithley E, Chen D, Ward EJ, Chinn SB, Friedman RA, Yu HT, Moriwaki K, Shiroishi T, Hamilton BA (November 2003). "A natural allele of Nxf1 suppresses retrovirus insertional mutations". Nat. Genet. 35 (3): 221â8. doi:10.1038/ng1247. PMC 2756099. PMID 14517553.
- Concepcion D, Flores-GarcÃa L, Hamilton BA (May 2009). "Multipotent genetic suppression of retrotransposon-induced mutations by Nxf1 through fine-tuning of alternative splicing". In Frankel, Wayne N. PLoS Genet. 5 (5): e1000484. doi:10.1371/journal.pgen.1000484. PMC 2674570. PMID 19436707.
- Shamsher, Monee K; Ploski Jonathan, Radu Aurelian (October 2002). "Karyopherin beta 2B participates in mRNA export from the nucleus". Proc. Natl. Acad. Sci. U.S.A. (United States) 99 (22): 14195â9. doi:10.1073/pnas.212518199. ISSN 0027-8424. PMC 137860. PMID 12384575.
- Kataoka, N; Diem M D, Kim V N, Yong J, Dreyfuss G (November 2001). "Magoh, a human homolog of Drosophila mago nashi protein, is a component of the splicing-dependent exon-exon junction complex". EMBO J. (England) 20 (22): 6424â33. doi:10.1093/emboj/20.22.6424. ISSN 0261-4189. PMC 125744. PMID 11707413.
- Zolotukhin, Andrei S; Tan Wei, Bear Jenifer, Smulevitch Sergey, Felber Barbara K (February 2002). "U2AF participates in the binding of TAP (NXF1) to mRNA". J. Biol. Chem. (United States) 277 (6): 3935â42. doi:10.1074/jbc.M107598200. ISSN 0021-9258. PMID 11724776.
- Tang, H; Wong-Staal F (October 2000). "Specific interaction between RNA helicase A and Tap, two cellular proteins that bind to the constitutive transport element of type D retrovirus". J. Biol. Chem. (UNITED STATES) 275 (42): 32694â700. doi:10.1074/jbc.M003933200. ISSN 0021-9258. PMID 10924507.
- Saito, Kuniaki; Fujiwara Toshinobu, Katahira Jun, Inoue Kunio, Sakamoto Hiroshi (August 2004). "TAP/NXF1, the primary mRNA export receptor, specifically interacts with a neuronal RNA-binding protein HuD". Biochem. Biophys. Res. Commun. (United States) 321 (2): 291â7. doi:10.1016/j.bbrc.2004.06.140. ISSN 0006-291X. PMID 15358174.
- Herold, A; Suyama M, Rodrigues J P, Braun I C, Kutay U, Carmo-Fonseca M, Bork P, Izaurralde E (December 2000). "TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture". Mol. Cell. Biol. (UNITED STATES) 20 (23): 8996â9008. doi:10.1128/MCB.20.23.8996-9008.2000. ISSN 0270-7306. PMC 86553. PMID 11073998.
- Schmitt, I; Gerace L (November 2001). "In vitro analysis of nuclear transport mediated by the C-terminal shuttle domain of Tap". J. Biol. Chem. (United States) 276 (45): 42355â63. doi:10.1074/jbc.M103916200. ISSN 0021-9258. PMID 11551912.
- Grant RP, Hurt E, Neuhaus D, Stewart M (April 2002). "Structure of the C-terminal FG-nucleoporin binding domain of Tap/NXF1". Nat. Struct. Biol. 9 (4): 247â51. doi:10.1038/nsb773. PMID 11875519.
- Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P (July 2000). "Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins". EMBO Rep. 1 (1): 53â8. doi:10.1038/sj.embor.embor627. PMC 1083685. PMID 11256625.
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TAP C-terminal domain Provide feedback
The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for nuclear export of mRNA. Tap has a modular structure, and its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling . The structure of the C-terminal domain is composed of four helices . The structure is related to the UBA domain.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005637
The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for nuclear export of mRNA. Tap has a modular structure, and its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [PUBMED:11875519]. The structure of the C-terminal domain is composed of four helices [PUBMED:11875519]. The structure is related to the UBA domain.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||nucleus (GO:0005634)|
|Biological process||mRNA transport (GO:0051028)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...
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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:||Bateman A|
|Number in seed:||8|
|Number in full:||365|
|Average length of the domain:||49.80 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||8.36 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|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:
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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.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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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.
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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.
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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.
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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 TAP_C domain has been found. There are 4 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.
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