Summary: TAP C-terminal domain
This is the Wikipedia entry entitled "NXF1". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at firstname.lastname@example.org and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
|Nuclear RNA export factor 1|
|Symbols||; MEX67; TAP|
|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 PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see [href="http://expasy.org/prosite/PDOC50177 PROSITEDOC]) 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): 571–82. doi:10.1016/S1074-7613(00)80345-3. PMID 9175835.
- Grüter 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): 649–59. doi:10.1016/S1097-2765(00)80065-9. PMID 9660949.
- Katahira J, Strässer 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): 2593–609. 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): 221–8. doi:10.1038/ng1247. PMC 2756099. PMID 14517553.
- Concepcion D, Flores-García 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): 14195–9. 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): 6424–33. 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): 3935–42. 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): 32694–700. 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): 291–7. 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): 8996–9008. 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): 42355–63. 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): 247–51. 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): 53–8. doi:10.1038/sj.embor.embor627. PMC 1083685. PMID 11256625.
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)|
- 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
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Bateman A|
|Number in seed:||170|
|Number in full:||629|
|Average length of the domain:||47.40 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||8.00 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
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
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.
Loading structure mapping...