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4  structures 218  species 0  interactions 365  sequences 19  architectures

Family: TAP_C (PF03943)

Summary: TAP C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "NXF1". More...

NXF1 Edit Wikipedia article

Nuclear RNA export factor 1

Rendering of 1FO1
Available structures
PDB Ortholog search: PDBe, RCSB
Identifiers
Symbols NXF1; MEX67; TAP
External IDs OMIM602647 MGI1858330 HomoloGene38176 GeneCards: NXF1 Gene
RNA expression pattern
PBB GE NXF1 208922 s at tn.png
PBB GE NXF1 220934 s at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 10482 53319
Ensembl ENSG00000162231 ENSMUSG00000010097
UniProt Q9UBU9 Q99JX7
RefSeq (mRNA) NM_001081491 NM_001276704
RefSeq (protein) NP_001074960 NP_001263633
Location (UCSC) Chr 11:
62.56 – 62.57 Mb
Chr 19:
8.76 – 8.77 Mb
PubMed search [1] [2]

Nuclear RNA export factor 1, also known as NXF1, is a protein which in humans is encoded by the NXF1 gene.[1][2]

Function[edit]

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.[2][3] 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.[4] 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.[5][6]

Interactions[edit]

NXF1 has been shown to interact with TNPO2,[7] MAGOH,[8] U2 small nuclear RNA auxiliary factor 1,[9] DHX9,[10] HuD[11] and NUP214.[12][13]

Tap protein[edit]

In molecular biology, another name for the protein NXF1 is TAP. In particular this entry focuses on the C-terminal domain, which also contains the UBA(protein domain).

TAP_C
PDB 1oai EBI.jpg
complex between tap uba domain and fxfg nucleoporin peptide
Identifiers
Symbol TAP_C
Pfam PF03943
Pfam clan CL0214
InterPro IPR005637
SCOP 1go5
SUPERFAMILY 1go5

This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include:

  • vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1).
  • Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1).

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.[14][15]

Function[edit]

Nuclear export of mRNAs is mediated by the Tap protein.

Structure[edit]

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.

References[edit]

  1. ^ 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. 
  2. ^ a b 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. 
  3. ^ 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. 
  4. ^ "Entrez Gene: NXF1 nuclear RNA export factor 1". 
  5. ^ 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. 
  6. ^ 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. 
  7. ^ 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. 
  8. ^ 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. 
  9. ^ 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. 
  10. ^ 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. 
  11. ^ 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. 
  12. ^ 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. 
  13. ^ 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. 
  14. ^ a b 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. 
  15. ^ a b 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. 


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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.

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 [1]. The structure of the C-terminal domain is composed of four helices [1]. The structure is related to the UBA domain.

Literature references

  1. Grant RP, Hurt E, Neuhaus D, Stewart M; , Nat Struct Biol 2002;9:247-251.: Structure of the C-terminal FG-nucleoporin binding domain of Tap/NXF1. PUBMED:11875519 EPMC:11875519


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.

Gene Ontology

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

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan UBA (CL0214), which has the following description:

This superfamily includes domains related to the UBA domain. These domains are often involved in ubiquitin binding.

The clan contains the following 9 members:

CUE DMA DUF1296 RuvA_C TAP_C UBA UBA_2 UBA_3 UBA_4

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...

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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.

  Seed
(8)
Full
(365)
Representative proteomes NCBI
(372)
Meta
(0)
RP15
(74)
RP35
(111)
RP55
(185)
RP75
(263)
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  Seed
(8)
Full
(365)
Representative proteomes NCBI
(372)
Meta
(0)
RP15
(74)
RP35
(111)
RP55
(185)
RP75
(263)
Alignment:
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Sequence:
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  Seed
(8)
Full
(365)
Representative proteomes NCBI
(372)
Meta
(0)
RP15
(74)
RP35
(111)
RP55
(185)
RP75
(263)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
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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 View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Domain
Author: 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 information View help on HMM parameters

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 21.3 21.3
Trusted cut-off 21.4 22.6
Noise cut-off 21.2 20.6
Model length: 51
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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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 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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