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22  structures 1430  species 0  interactions 3054  sequences 55  architectures

Family: TFIID-18kDa (PF02269)

Summary: Transcription initiation factor IID, 18kD subunit

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This is the Wikipedia entry entitled "TBP-associated factor". More...

TBP-associated factor Edit Wikipedia article

TBP associated factor (TAF6)
PDB 1taf EBI.jpg
drosophila dtafii42/dtafii62 (like TAF6/TAF9) heterotetramer, HFD
Identifiers
SymbolTAF
PfamPF02969
Pfam clanCL0012
InterProIPR004823
SCOP21bh9 / SCOPe / SUPFAM

The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.

TAFs have a signature N-terminal histone-like fold domain (HFD).[1] This domain is implicated in the pairwise interaction among specific TAFs.[2]

Function

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).[3]

TAF is part of the TFIID complex, and interacts 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 contribute transcription activation and to promoter selectivity.[3]

Some pairs of TAF interact with each other to form "lobes" in TFIID. Pairs known or suggested to exist in TFIID include TAF6-TAF9, TAF4-TAF12, TAF11-13, TAF8-TAF10 and TAF3-TAF10.[2]

SL1

Selective factor 1 is composed of the TATA-binding protein and three TAF (TATA box-binding protein-associated factor) subunits (TAF1A, TAF1B, and TAF1C). These TAFs do not have a histone-like fold domain.[4]

Other complexes

TAF is a part of SAGA (SPT-ADA-GCN5 acetylase) and related coactivation complexes.[2] Such complexes acetylate histone tails to activate genes.[5] Human has three SAGA-like complexes: PCAF, TFTC (TBP-free TAF-containing complex), and STAGA (SPT3-TAF9-GCN5L acetylase). PCAF (GCN5) and KAT2A (GCN5L) are two human homologs of the yeast Gcn5.[6]

TAF8, TAF10, and SPT7L forms a small TAF complex called SMAT.[2]

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.[1]

Human genes

Assorted signatures

TAF domains are spread out across many digital signatures:

TAF4
Identifiers
SymbolTAF4
PfamPF05236
InterProIPR007900
TAF
Identifiers
Symbol?
PfamPF04719
TAF13
Identifiers
SymbolTFIID-18kDa
PfamPF02269
InterProIPR003195
TAFII31 (TAF9)
Identifiers
SymbolTFIID-31kDa
PfamPF02291
InterProIPR003162
TAF
Identifiers
Symbol?
PfamPF03847
TAF
Identifiers
Symbol?
PfamPF03540
TAF/Nervy homology (TAF4/4B)
Identifiers
SymbolTAFH
PfamPF07531
InterProIPR003894
SMARTTAFH
TAF RNA Polymerase I subunit A (TAF1A)
Identifiers
SymbolTAF1_subA
PfamPF14929
InterProIPR039495

References

  1. ^ a b Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT, Roeder RG, Nakatani Y, Burley SK (March 1996). "Structural similarity between TAFs and the heterotetrameric core of the histone octamer". Nature. 380 (6572): 316–22. Bibcode:1996Natur.380..316X. doi:10.1038/380316a0. PMID 8598927. S2CID 4329570.
  2. ^ a b c d Demény MA, Soutoglou E, Nagy Z, Scheer E, Jànoshàzi A, Richardot M, Argentini M, Kessler P, Tora L (March 2007). "Identification of a small TAF complex and its role in the assembly of TAF-containing complexes". PLOS ONE. 2 (3): e316. Bibcode:2007PLoSO...2..316D. doi:10.1371/journal.pone.0000316. PMC 1820849. PMID 17375202.
  3. ^ a b Furukawa T, Tanese N (September 2000). "Assembly of partial TFIID complexes in mammalian cells reveals distinct activities associated with individual TATA box-binding protein-associated factors". The Journal of Biological Chemistry. 275 (38): 29847–56. doi:10.1074/jbc.M002989200. PMID 10896937.
  4. ^ Friedrich JK, Panov KI, Cabart P, Russell J, Zomerdijk JC (August 2005). "TBP-TAF complex SL1 directs RNA polymerase I pre-initiation complex formation and stabilizes upstream binding factor at the rDNA promoter". The Journal of Biological Chemistry. 280 (33): 29551–8. doi:10.1074/jbc.M501595200. PMC 3858828. PMID 15970593.
  5. ^ Bonnet J, Wang CY, Baptista T, Vincent SD, Hsiao WC, Stierle M, Kao CF, Tora L, Devys D (September 2014). "The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription". Genes & Development. 28 (18): 1999–2012. doi:10.1101/gad.250225.114. PMC 4173158. PMID 25228644.
  6. ^ Martinez E, Palhan VB, Tjernberg A, Lymar ES, Gamper AM, Kundu TK, Chait BT, Roeder RG (October 2001). "Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo". Molecular and Cellular Biology. 21 (20): 6782–95. doi:10.1128/MCB.21.20.6782-6795.2001. PMC 99856. PMID 11564863.
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Transcription initiation factor IID, 18kD subunit Provide feedback

This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [1]

Literature references

  1. Birck C, Poch O, Romier C, Ruff M, Mengus G, Lavigne AC, Davidson I, Moras D; , Cell 1998;94:239-249.: Human TAF(II)28 and TAF(II)18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family. PUBMED:9695952 EPMC:9695952


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003195

This family includes the Spt3 yeast transcription factors and the 18kDa subunit from human transcription initiation factor IID, known as TAF13 or TAFII18. Determination of the crystal structure reveals an atypical histone fold [ PUBMED:9695952 ].

TBP-associated factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the transcription factor IID (TFIID) complex. TAF13 interacts with TAF11 and makes a histone-like heterodimer similar to H3/H4-like proteins. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex [ PUBMED:9695952 ].

TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in 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. TFIID complex is composed of the TBP and at least 13 TAFs. Each TAF, with the help of a specific activator, is required only for expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and are found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure.

Gene Ontology

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Domain organisation

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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_30kDa

Alignments

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(4897)
RP15
(618)
RP35
(1355)
RP55
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RP75
(3114)
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Trees

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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: Pfam-B_3681 (release 5.2)
Previous IDs: TFIID-18;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Mian N
Number in seed: 6
Number in full: 3054
Average length of the domain: 88.20 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 33.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.1 27.1
Noise cut-off 26.9 26.9
Model length: 93
Family (HMM) version: 19
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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-18kDa domain has been found. There are 22 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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