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2  structures 691  species 3  interactions 1027  sequences 15  architectures

Family: TAF4 (PF05236)

Summary: Transcription initiation factor TFIID component TAF4 family

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 "TAF4". More...

TAF4 Edit Wikipedia article

TAF4
Protein TAF4 PDB 1h3o.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases TAF4, TAF2C, TAF2C1, TAF4A, TAFII130, TAFII135, TATA-box binding protein associated factor 4
External IDs MGI: 2152346 HomoloGene: 55723 GeneCards: TAF4
Gene location (Human)
Chromosome 20 (human)
Chr. Chromosome 20 (human)[1]
Chromosome 20 (human)
Genomic location for TAF4
Genomic location for TAF4
Band 20q13.33 Start 61,953,469 bp[1]
End 62,065,810 bp[1]
RNA expression pattern
PBB GE TAF4 208545 x at fs.png

PBB GE TAF4 213090 s at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_003185

NM_001081092

RefSeq (protein)

NP_003176

NP_001074561

Location (UCSC) Chr 20: 61.95 – 62.07 Mb Chr 20: 179.91 – 179.98 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Transcription initiation factor TFIID subunit 4 is a protein that in humans is encoded by the TAF4 gene.[5][6][7]

Function

Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes one of the larger subunits of TFIID that has been shown to potentiate transcriptional activation by retinoic acid, thyroid hormone and vitamin D3 receptors. In addition, this subunit interacts with the transcription factor CREB, which has a glutamine-rich activation domain, and binds to other proteins containing glutamine-rich regions. Aberrant binding to this subunit by proteins with expanded polyglutamine regions has been suggested as one of the pathogenetic mechanisms underlying a group of neurodegenerative disorders referred to as polyglutamine diseases.[7]

Interactions

TAF4 has been shown to interact with:

Protein domain

TAF4
PDB 1h3o EBI.jpg
crystal structure of the human taf4-taf12 (tafii135-tafii20) complex
Identifiers
Symbol TAF4
Pfam PF05236
InterPro IPR007900
SCOP 1h3o
SUPERFAMILY 1h3o

Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4.[12]

References

  1. ^ a b c ENSG00000130699 GRCh38: Ensembl release 89: ENSG00000280529, ENSG00000130699 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000039117 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ Tanese N, Saluja D, Vassallo MF, Chen JL, Admon A (1996). "Molecular cloning and analysis of two subunits of the human TFIID complex: hTAFII130 and hTAFII100". Proc. Natl. Acad. Sci. U.S.A. 93 (24): 13611–6. doi:10.1073/pnas.93.24.13611. PMC 19367Freely accessible. PMID 8942982. 
  6. ^ Mengus G, May M, Carré L, Chambon P, Davidson I (July 1997). "Human TAF(II)135 potentiates transcriptional activation by the AF-2s of the retinoic acid, vitamin D3, and thyroid hormone receptors in mammalian cells". Genes Dev. 11 (11): 1381–95. doi:10.1101/gad.11.11.1381. PMID 9192867. 
  7. ^ a b "Entrez Gene: TAF4 TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa". 
  8. ^ Vassallo MF, Tanese N (April 2002). "Isoform-specific interaction of HP1 with human TAFII130". Proc. Natl. Acad. Sci. U.S.A. 99 (9): 5919–24. doi:10.1073/pnas.092025499. PMC 122877Freely accessible. PMID 11959914. 
  9. ^ Pointud JC, Mengus G, Brancorsini S, Monaco L, Parvinen M, Sassone-Corsi P, Davidson I (May 2003). "The intracellular localisation of TAF7L, a paralogue of transcription factor TFIID subunit TAF7, is developmentally regulated during male germ-cell differentiation". J. Cell Sci. 116 (Pt 9): 1847–58. doi:10.1242/jcs.00391. PMID 12665565. 
  10. ^ Bellorini M, Lee DK, Dantonel JC, Zemzoumi K, Roeder RG, Tora L, Mantovani R (June 1997). "CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues". Nucleic Acids Res. 25 (11): 2174–81. doi:10.1093/nar/25.11.2174. PMC 146709Freely accessible. PMID 9153318. 
  11. ^ Brand M, Moggs JG, Oulad-Abdelghani M, Lejeune F, Dilworth FJ, Stevenin J, Almouzni G, Tora L (June 2001). "UV-damaged DNA-binding protein in the TFTC complex links DNA damage recognition to nucleosome acetylation". EMBO J. 20 (12): 3187–96. doi:10.1093/emboj/20.12.3187. PMC 150203Freely accessible. PMID 11406595. 
  12. ^ Thuault S, Gangloff YG, Kirchner J, Sanders S, Werten S, Romier C, Weil PA, Davidson I (November 2002). "Functional analysis of the TFIID-specific yeast TAF4 (yTAF(II)48) reveals an unexpected organization of its histone-fold domain". J. Biol. Chem. 277 (47): 45510–7. doi:10.1074/jbc.M206556200. PMID 12237303. 

Further reading

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Transcription initiation factor TFIID component TAF4 family Provide feedback

This region of similarity is found in Transcription initiation factor TFIID component TAF4 [1].

Literature references

  1. Thuault S, Gangloff YG, Kirchner J, Sanders S, Werten S, Romier C, Weil PA, Davidson I; , J Biol Chem 2002;277:45510-45517.: Functional analysis of the TFIID-specific yeast TAF4 (yTAF(II)48) reveals an unexpected organization of its histone-fold domain. PUBMED:12237303 EPMC:12237303


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007900

Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains. The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 [PUBMED:12237303].

TAF4 domain interacts with TAF12 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes [PUBMED:19635797, PUBMED:12237304].

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 Histone (CL0012), which has the following description:

Members of this clan all possess a histone fold. Generally proteins in this clan are DNA binding.

The clan contains the following 15 members:

Bromo_TP Bromo_TP_like CBFD_NFYB_HMF CENP-S CENP-T_C CENP-W CENP-X DUF1931 Histone TAF TAF4 TAFII28 TFIID-18kDa TFIID-31kDa TFIID_20kDa

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 (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. 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
(80)
Full
(1027)
Representative proteomes UniProt
(1517)
NCBI
(2385)
Meta
(0)
RP15
(214)
RP35
(477)
RP55
(775)
RP75
(974)
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Key: ✓ available, x not generated, not available.

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  Seed
(80)
Full
(1027)
Representative proteomes UniProt
(1517)
NCBI
(2385)
Meta
(0)
RP15
(214)
RP35
(477)
RP55
(775)
RP75
(974)
Alignment:
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Sequence:
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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.

  Seed
(80)
Full
(1027)
Representative proteomes UniProt
(1517)
NCBI
(2385)
Meta
(0)
RP15
(214)
RP35
(477)
RP55
(775)
RP75
(974)
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.

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: Wood V
Previous IDs: none
Type: Family
Author: Wood V
Number in seed: 80
Number in full: 1027
Average length of the domain: 253.80 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 40.52 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 31.8 31.8
Trusted cut-off 31.8 31.8
Noise cut-off 31.7 31.7
Model length: 278
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 3 interactions for this family. More...

TAF4 TFIID_20kDa TFIID_20kDa

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 TAF4 domain has been found. There are 2 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 sequence.

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