TATA-binding protein

Last updated

TBP
Protein TBP PDB 1c9b.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases TBP , GTF2D, GTF2D1, HDL4, SCA17, TFIID, TATA-box binding protein, TATA-binding protein, TBP1
External IDs OMIM: 600075 MGI: 101838 HomoloGene: 2404 GeneCards: TBP
Orthologs
SpeciesHumanMouse
Entrez

6908

21374

Ensembl

ENSG00000112592

ENSMUSG00000014767

UniProt

P20226

P29037

RefSeq (mRNA)

NM_003194
NM_001172085

NM_013684

RefSeq (protein)

NP_001165556
NP_003185

NP_038712

Location (UCSC) Chr 6: 170.55 – 170.57 Mb Chr 17: 15.72 – 15.75 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse
TBP
PDB 1ngm EBI.jpg
crystal structure of a yeast brf1-tbp-dna ternary complex
Identifiers
SymbolTBP
Pfam PF00352
Pfam clan CL0407
InterPro IPR000814
PROSITE PDOC00303
SCOP2 1tbp / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary

The TATA-binding protein (TBP) is a general transcription factor that binds to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters. [5]

TBP gene family

TBP is a member of a small gene family of TBP-related factors. [6] The first TBP-related factor (TRF/TRF1) was identified in the fruit fly Drosophila, but appears to be fly or insect-specific. Subsequently TBPL1/TRF2 was found in the genomes of many metazoans, whereas vertebrate genomes encode a third vertebrate family member, TBPL2/TRF3. In specific cell types or on specific promoters TBP can be replaced by one of these TBP-related factors, some of which interact with the TATA box similarly to TBP.

Role as transcription factor

TBP is a subunit of the eukaryotic general transcription factor TFIID. TFIID is the first protein to bind to DNA during the formation of the transcription preinitiation complex of RNA polymerase II (RNA Pol II). [7] As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. However, it is estimated that only 10–20% of human promoters have TATA boxes - the majority of human promoters are TATA-less housekeeping gene promoters - so TBP is probably not the only protein involved in positioning RNA polymerase II.. The binding of TBP to these promoters is facilitated by housekeeping gene regulators. [8] [9] Interestingly, transcription initiates within a narrow region at around 30 bp downstream of TATA box on TATA-containing promoters, [10] while transcription start sites of TATA-less promoters are dispersed within a 200 bp region. [11] [9]

Binding of TFIID to the TATA box in the promoter region of the gene initiates the recruitment of other factors required for RNA Pol II to begin transcription. Some of the other recruited transcription factors include TFIIA, TFIIB, and TFIIF. Each of these transcription factors contains several protein subunits.

TBP is also important for transcription by RNA polymerase I and RNA polymerase III, and is therefore involved in transcription initiation by all three RNA polymerases. [12]

TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β sheet.

Another distinctive feature of TBP is a long string of glutamines in the N-terminus of the protein. This region modulates the DNA binding activity of the C-terminus, and modulation of DNA-binding affects the rate of transcription complex formation and initiation of transcription. Mutations that expand the number of CAG repeats encoding this polyglutamine tract, and thus increase the length of the polyglutamine string, are associated with spinocerebellar ataxia 17, a neurodegenerative disorder classified as a polyglutamine disease. [13]

DNA-protein interactions

When TBP binds to a TATA box within the DNA, it distorts the DNA by inserting amino acid side-chains between base pairs, partially unwinding the helix, and doubly kinking it. The distortion is accomplished through a great amount of surface contact between the protein and DNA. TBP binds with the negatively charged phosphates in the DNA backbone through positively charged lysine and arginine amino acid residues. The sharp bend in the DNA is produced through projection of four bulky phenylalanine residues into the minor groove. As the DNA bends, its contact with TBP increases, thus enhancing the DNA-protein interaction.

The strain imposed on the DNA through this interaction initiates melting, or separation, of the strands. Because this region of DNA is rich in adenine and thymine residues, which base-pair through only two hydrogen bonds, the DNA strands are more easily separated. Separation of the two strands exposes the bases and allows RNA polymerase II to begin transcription of the gene.

TBP's C-terminus composes of a helicoidal shape that (incompletely) complements the T-A-T-A region of DNA. This incompleteness allows DNA to be passively bent on binding.

For information on the use of TBP in cells see: RNA polymerase I, RNA polymerase II, and RNA polymerase III.

Protein–protein interactions

TATA-binding protein has been shown to interact with:

Complex assembly

The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box. [51] [52] In the presence of a TATA-less promoter, TBP binds with the help of TBP-associated factors (TAFs). [53] [54] TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins. [55]

Structure

The C-terminal core of TBP (~180 residues) is highly conserved and contains two 88-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins . [56] By contrast, the N-terminal region varies in both length and sequence.

Related Research Articles

In molecular biology, the TATA box is a sequence of DNA found in the core promoter region of genes in archaea and eukaryotes. The bacterial homolog of the TATA box is called the Pribnow box which has a shorter consensus sequence.

<span class="mw-page-title-main">General transcription factor</span> Class of protein transcription factors

General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA. GTFs, RNA polymerase, and the mediator constitute the basic transcriptional apparatus that first bind to the promoter, then start transcription. GTFs are also intimately involved in the process of gene regulation, and most are required for life.

Transcription factor II D (TFIID) is one of several general transcription factors that make up the RNA polymerase II preinitiation complex. RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins. Before the start of transcription, the transcription Factor II D (TFIID) complex binds to the core promoter DNA of the gene through specific recognition of promoter sequence motifs, including the TATA box, Initiator, Downstream Promoter, Motif Ten, or Downstream Regulatory elements.

Transcription factor TFIIA is a nuclear protein involved in the RNA polymerase II-dependent transcription of DNA. TFIIA is one of several general (basal) transcription factors (GTFs) that are required for all transcription events that use RNA polymerase II. Other GTFs include TFIID, a complex composed of the TATA binding protein TBP and TBP-associated factors (TAFs), as well as the factors TFIIB, TFIIE, TFIIF, and TFIIH. Together, these factors are responsible for promoter recognition and the formation of a transcription preinitiation complex (PIC) capable of initiating RNA synthesis from a DNA template.

<span class="mw-page-title-main">TAF6</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 6 is a protein that in humans is encoded by the TAF6 gene.

<span class="mw-page-title-main">TAF7</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 7 also known as TAFII55 is a protein that in humans is encoded by the TAF7 gene.

<span class="mw-page-title-main">TAF1</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 1, also known as transcription initiation factor TFIID 250 kDa subunit (TAFII-250) or TBP-associated factor 250 kDa (p250), is a protein that in humans is encoded by the TAF1 gene.

<span class="mw-page-title-main">TAF9</span> Protein-coding gene in the species Homo sapiens

TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa, also known as TAF9, is a protein that in humans is encoded by the TAF9 gene.

<span class="mw-page-title-main">TAF12</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 12 is a protein that in humans is encoded by the TAF12 gene.

<span class="mw-page-title-main">TAF4</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 4 is a protein that in humans is encoded by the TAF4 gene.

<span class="mw-page-title-main">TAF2</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 2 is a protein that in humans is encoded by the TAF2 gene.

<span class="mw-page-title-main">TAF10</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 10 is a protein that in humans is encoded by the TAF10 gene.

<span class="mw-page-title-main">TAF5</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 5 is a protein that in humans is encoded by the TAF5 gene.

<span class="mw-page-title-main">TAF11</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 11 also known as TAFII28, is a protein that in humans is encoded by the TAF11 gene.

<span class="mw-page-title-main">TAF15</span> Protein-coding gene in the species Homo sapiens

TATA-binding protein-associated factor 2N is a protein that in humans is encoded by the TAF15 gene.

<span class="mw-page-title-main">TAF13</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 13 is a protein that in humans is encoded by the TAF13 gene.

<span class="mw-page-title-main">TAF8</span> Protein-coding gene in the species Homo sapiens

Transcription initiation factor TFIID subunit 8 is a protein that in humans is encoded by the TAF8 gene.

<span class="mw-page-title-main">TAF1C</span> Protein-coding gene in the species Homo sapiens

TATA box-binding protein-associated factor RNA polymerase I subunit C is an enzyme that in humans is encoded by the TAF1C gene.

<span class="mw-page-title-main">TAF1B</span> Protein-coding gene in the species Homo sapiens

TATA box-binding protein-associated factor RNA polymerase I subunit B is an enzyme that in humans is encoded by the TAF1B gene.

<span class="mw-page-title-main">TBP-associated factor</span> Protein domains

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.

References

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  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000014767 - Ensembl, May 2017
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