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18  structures 1387  species 0  interactions 1750  sequences 39  architectures

Family: TAFII28 (PF04719)

Summary: hTAFII28-like protein conserved region

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 "TAF11". More...

TAF11 Edit Wikipedia article

TAF11
Protein TAF11 PDB 1bh8.png
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesTAF11, MGC:15243, TAF2I, TAFII28, PRO2134, TATA-box binding protein associated factor 11
External IDsOMIM: 600772 MGI: 1916026 HomoloGene: 55918 GeneCards: TAF11
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001270488
NM_005643

NM_026836
NM_001379368

RefSeq (protein)

NP_001257417
NP_005634

NP_081112
NP_001366297

Location (UCSC)Chr 6: 34.88 – 34.89 MbChr 17: 27.9 – 27.91 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Transcription initiation factor TFIID subunit 11 also known as TAFII28, is a protein that in humans is encoded by the TAF11 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 a small subunit of TFIID that is present in all TFIID complexes and interacts with TBP. This subunit also interacts with another small subunit, TAF13, to form a heterodimer with a structure similar to the histone core structure.[7]

TAFII28
PDB 1bh9 EBI.jpg
htafii18/htafii28 heterodimer crystal structure with bound pcmbs
Identifiers
SymbolTAFII28
PfamPF04719
Pfam clanCL0012
InterProIPR006809
SCOP21bh9 / SCOPe / SUPFAM

In molecular biology, TAFII28 refers to the TATA box binding protein associated factor. Together with the TATA-binding protein and other TAFs it forms the general transcription factor, TFIID. They together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins.

Structure

The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3.[5][8]

Interactions

TAF11 has been shown to interact with:

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000064995 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000024218 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b c d Mengus G, May M, Jacq X, Staub A, Tora L, Chambon P, Davidson I (May 1995). "Cloning and characterization of hTAFII18, hTAFII20 and hTAFII28: three subunits of the human transcription factor TFIID". EMBO J. 14 (7): 1520–31. doi:10.1002/j.1460-2075.1995.tb07138.x. PMC 398239. PMID 7729427.
  6. ^ Kuzuhara T, Horikoshi M (November 1996). "Isolation and characterization of a cDNA encoding a human TFIID subunit containing a variety of putative structural motifs including direct repeats". Biol. Pharm. Bull. 19 (1): 122–6. doi:10.1248/bpb.19.122. PMID 8820923.
  7. ^ a b "Entrez Gene: TAF11 TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa".
  8. ^ a b Birck C, Poch O, Romier C, Ruff M, Mengus G, Lavigne AC, Davidson I, Moras D (July 1998). "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". Cell. 94 (2): 239–49. doi:10.1016/S0092-8674(00)81423-3. PMID 9695952. S2CID 6274415.
  9. ^ a b c Scully R, Anderson SF, Chao DM, Wei W, Ye L, Young RA, Livingston DM, Parvin JD (May 1997). "BRCA1 is a component of the RNA polymerase II holoenzyme". Proc. Natl. Acad. Sci. U.S.A. 94 (11): 5605–10. Bibcode:1997PNAS...94.5605S. doi:10.1073/pnas.94.11.5605. PMC 20825. PMID 9159119.
  10. ^ Bertolotti A, Melot T, Acker J, Vigneron M, Delattre O, Tora L (March 1998). "EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes". Mol. Cell. Biol. 18 (3): 1489–97. doi:10.1128/mcb.18.3.1489. PMC 108863. PMID 9488465.
  11. ^ 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 146709. PMID 9153318.
  12. ^ May M, Mengus G, Lavigne AC, Chambon P, Davidson I (June 1996). "Human TAF(II28) promotes transcriptional stimulation by activation function 2 of the retinoid X receptors". EMBO J. 15 (12): 3093–104. doi:10.1002/j.1460-2075.1996.tb00672.x. PMC 450252. PMID 8670810.

Further reading

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

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.
This article incorporates text from the public domain Pfam and InterPro:

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.

hTAFII28-like protein conserved region Provide feedback

The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C-terminal of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [1,2].

Literature references

  1. Mengus G, May M, Jacq X, Staub A, Tora L, Chambon P, Davidson I; , EMBO J 1995;14:1520-1531.: Cloning and characterization of hTAFII18, hTAFII20 and hTAFII28: three subunits of the human transcription factor TFIID. PUBMED:7729427 EPMC:7729427

  2. 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 IPR006809

The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [ PUBMED:7729427 , PUBMED:9695952 ].

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 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

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 and the UniProtKB sequence database. More...

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  Seed
(77)
Full
(1750)
Representative proteomes UniProt
(2878)
RP15
(374)
RP35
(823)
RP55
(1341)
RP75
(1798)
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  Seed
(77)
Full
(1750)
Representative proteomes UniProt
(2878)
RP15
(374)
RP35
(823)
RP55
(1341)
RP75
(1798)
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  Seed
(77)
Full
(1750)
Representative proteomes UniProt
(2878)
RP15
(374)
RP35
(823)
RP55
(1341)
RP75
(1798)
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.

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.

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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_4085 (release 7.5)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Waterfield DI , Finn RD
Number in seed: 77
Number in full: 1750
Average length of the domain: 92.70 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 32.19 %

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 27.0 27.1
Noise cut-off 26.7 26.7
Model length: 86
Family (HMM) version: 17
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 TAFII28 domain has been found. There are 18 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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