Summary: Transcription initiation factor TFIID subunit A
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TBP-associated factor Edit Wikipedia article
TAF | |||||||||
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![]() drosophila tbp associated factors dtafii42/dtafii62 heterotetramer | |||||||||
Identifiers | |||||||||
Symbol | TAF | ||||||||
Pfam | PF02969 | ||||||||
Pfam clan | CL0012 | ||||||||
InterPro | IPR004823 | ||||||||
SMART | TAFH | ||||||||
SCOP2 | 1bh9 / SCOPe / SUPFAM | ||||||||
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In molecular biology, this entry, TAF refers to a protein named the TATA box binding protein associated factor. TAF is part of the transcription initiation factor TFIID multimeric protein complex, or in simpler terms, the Pre-initiation complex (PIC). TAF forms part of Transcription factor II D (TFIID) and the TATA-binding protein (TBP). They mediate transcription of DNA to RNA by RNA PolymeraseRNA polymerase II. This entry discusses the N-terminal domain in particular.
TFIID
TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS)[1]. TAF proteins adopt a histone-like fold.
TAF function
There are several function of TAF in its role as part of the TFIID complex, their function is to interact with the following
- specific transcriptional activators,
- basal transcription factors,
- other TAFIIs,
- specific DNA sequences, for example the downstream promoter element or gene-specific core promoter sequence.
Due to such interactions, they therefore contribute transcription activation and to promoter selectivity. [1]
TAF structure
The N-terminal domain of TAF has a histone-like protein fold. It contains two short alpha helices and a long central alpha helix. [2]
Types of TAF
- TAF1 (TAFII250)
- TAF2 (CIF150)
- TAF3 (TAFII140)
- TAF4 (TAFII130/135)
- TAF4B (TAFII105)
- TAF5 (TAFII100)
- TAF6 (TAFII70/80)
- TAF7 (TAFII55)
- TAF8 (TAFII43)
- TAF9 (TAFII31/32)
- TAF9B (TAFII31L)
- TAF10 (TAFII30)
- TAF11 (TAFII28)
- TAF12 (TAFII20/15)
- TAF13 (TAFII18)
- TAF15 (TAFII68)
References
- ^ a b Furukawa T, Tanese N (2000). "Assembly of partial TFIID complexes in mammalian cells reveals distinct activities associated with individual TATA box-binding protein-associated factors". J Biol Chem. 275 (38): 29847–56. doi:10.1074/jbc.M002989200. PMID 10896937.
- ^ Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT; et al. (1996). "Structural similarity between TAFs and the heterotetrameric core of the histone octamer". Nature. 380 (6572): 316–22. doi:10.1038/380316a0. PMID 8598927.
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Transcription initiation factor TFIID subunit A Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | Bromo_TP CBFD_NFYB_HMF CENP-S CENP-T_C Histone TAF TFIID-18kDa TFIID-31kDa |
Similarity to PfamA using HHSearch: | Histone CBFD_NFYB_HMF |
External database links
SCOP: | 1h3o |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003228
TFIID is one of several General Transcription Factors (GTFs), which also include TFIIA, TFIIB, TFIIE, TFIIF and TFIIH, that are involved in the accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. Human transcription initiation factor TFIID is composed of the TATA-binding protein (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [ PUBMED:7667268 , PUBMED:10664584 ].
TBP-associated factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TAF12 interacts with TAF4 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes [ PUBMED:19635797 ].
This entry represents a domain found in TAF12.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | transcription factor TFIID complex (GO:0005669) |
Biological process | DNA-templated transcription, initiation (GO:0006352) |
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 17 members:
Bromo_TP Bromo_TP_like CBFD_NFYB_HMF CENP-S CENP-T_C CENP-W CENP-X DUF1931 Histone PAF TAF TAF4 TAFII28 TFIID-18kDa TFIID-31kDa TFIID_20kDa TFIID_30kDaAlignments
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Seed (8) |
Full (2120) |
Representative proteomes | UniProt (3386) |
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RP15 (429) |
RP35 (1014) |
RP55 (1656) |
RP75 (2198) |
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PP/heatmap | 1 |
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Seed (8) |
Full (2120) |
Representative proteomes | UniProt (3386) |
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RP15 (429) |
RP35 (1014) |
RP55 (1656) |
RP75 (2198) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Curation and family details
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Curation
Seed source: | PRODOM |
Previous IDs: | TFIID_A; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Griffiths-Jones SR |
Number in seed: | 8 |
Number in full: | 2120 |
Average length of the domain: | 68.1 aa |
Average identity of full alignment: | 47 % |
Average coverage of the sequence by the domain: | 15.62 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 68 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
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 TFIID_20kDa domain has been found. There are 40 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.