TBP
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesTBP, GTF2D, GTF2D1, HDL4, SCA17, TFIID, TATA-box binding protein, TATA-binding protein, TBP1
External IDsOMIM: 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 MbChr 17: 15.72 – 15.75 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse
TBP
crystal structure of a yeast brf1-tbp-dna ternary complex
Identifiers
SymbolTBP
PfamPF00352
Pfam clanCL0407
InterProIPR000814
PROSITEPDOC00303
SCOP21tbp / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

The TATA-binding protein (TBP) is a general transcription factor that binds specifically 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.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000112592 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000014767 - 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. ↑ Kornberg RD (2007). "The molecular basis of eukaryotic transcription". Proc. Natl. Acad. Sci. U.S.A. 104 (32): 12955–61. Bibcode:2007PNAS..10412955K. doi:10.1073/pnas.0704138104. PMC 1941834. PMID 17670940.
  6. ↑ Akhtar W, Veenstra GJ (1 January 2011). "TBP-related factors: a paradigm of diversity in transcription initiation". Cell & Bioscience. 1 (1): 23. doi:10.1186/2045-3701-1-23. PMC 3142196. PMID 21711503.
  7. ↑ Lee TI, Young RA (2000). "Transcription of eukaryotic protein-coding genes". Annual Review of Genetics. 34: 77–137. doi:10.1146/annurev.genet.34.1.77. PMID 11092823.
  8. ↑ Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A (2012). "The NSL complex regulates housekeeping genes in Drosophila". PLOS Genetics. 8 (6): e1002736. doi:10.1371/journal.pgen.1002736. PMC 3375229. PMID 22723752.
  9. 1 2 Lam KC, Chung HR, Semplicio G, Iyer SS, Gaub A, Bhardwaj V, Holz H, Georgiev P, Akhtar A (February 2019). "The NSL complex-mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise". Genes & Development. 33 (7–8): 452–465. doi:10.1101/gad.321489.118. PMC 6446542. PMID 30819819.
  10. ↑ Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, et al. (June 2006). "Genome-wide analysis of mammalian promoter architecture and evolution". Nature Genetics. 38 (6): 626–35. doi:10.1038/ng1789. PMID 16645617. S2CID 22205897.
  11. ↑ Ni T, Corcoran DL, Rach EA, Song S, Spana EP, Gao Y, Ohler U, Zhu J (July 2010). "A paired-end sequencing strategy to map the complex landscape of transcription initiation". Nature Methods. 7 (7): 521–7. doi:10.1038/nmeth.1464. PMC 3197272. PMID 20495556.
  12. ↑ Vannini A, Cramer P (February 2012). "Conservation between the RNA polymerase I, II, and III transcription initiation machineries". Molecular Cell. 45 (4): 439–46. doi:10.1016/j.molcel.2012.01.023. hdl:11858/00-001M-0000-0015-483A-5. PMID 22365827.
  13. ↑ "Entrez Gene: TBP TATA box binding protein".
  14. ↑ McCulloch V, Hardin P, Peng W, Ruppert JM, Lobo-Ruppert SM (August 2000). "Alternatively spliced hBRF variants function at different RNA polymerase III promoters". EMBO J. 19 (15): 4134–43. doi:10.1093/emboj/19.15.4134. PMC 306597. PMID 10921893.
  15. ↑ Wang Z, Roeder RG (July 1995). "Structure and function of a human transcription factor TFIIIB subunit that is evolutionarily conserved and contains both TFIIB- and high-mobility-group protein 2-related domains". Proc. Natl. Acad. Sci. U.S.A. 92 (15): 7026–30. Bibcode:1995PNAS...92.7026W. doi:10.1073/pnas.92.15.7026. PMC 41464. PMID 7624363.
  16. 1 2 3 4 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.
  17. ↑ Chicca JJ, Auble DT, Pugh BF (March 1998). "Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1". Mol. Cell. Biol. 18 (3): 1701–10. doi:10.1128/MCB.18.3.1701. PMC 108885. PMID 9488487.
  18. ↑ Metz R, Bannister AJ, Sutherland JA, Hagemeier C, O'Rourke EC, Cook A, Bravo R, Kouzarides T (September 1994). "c-Fos-induced activation of a TATA-box-containing promoter involves direct contact with TATA-box-binding protein". Mol. Cell. Biol. 14 (9): 6021–9. doi:10.1128/MCB.14.9.6021. PMC 359128. PMID 8065335.
  19. ↑ Franklin CC, McCulloch AV, Kraft AS (February 1995). "In vitro association between the Jun protein family and the general transcription factors, TBP and TFIIB". Biochem. J. 305 (3): 967–74. doi:10.1042/bj3050967. PMC 1136352. PMID 7848298.
  20. ↑ Brendel C, Gelman L, Auwerx J (June 2002). "Multiprotein bridging factor-1 (MBF-1) is a cofactor for nuclear receptors that regulate lipid metabolism". Mol. Endocrinol. 16 (6): 1367–77. doi:10.1210/mend.16.6.0843. PMID 12040021.
  21. ↑ Mariotti M, De Benedictis L, Avon E, Maier JA (August 2000). "Interaction between endothelial differentiation-related factor-1 and calmodulin in vitro and in vivo". J. Biol. Chem. 275 (31): 24047–51. doi:10.1074/jbc.M001928200. PMID 10816571.
  22. ↑ Kabe Y, Goto M, Shima D, Imai T, Wada T, Morohashi Ki, Shirakawa M, Hirose S, Handa H (November 1999). "The role of human MBF1 as a transcriptional coactivator". J. Biol. Chem. 274 (48): 34196–202. doi:10.1074/jbc.274.48.34196. PMID 10567391.
  23. 1 2 Tang H, Sun X, Reinberg D, Ebright RH (February 1996). "Protein–protein interactions in eukaryotic transcription initiation: structure of the preinitiation complex". Proc. Natl. Acad. Sci. U.S.A. 93 (3): 1119–24. Bibcode:1996PNAS...93.1119T. doi:10.1073/pnas.93.3.1119. PMC 40041. PMID 8577725.
  24. ↑ Bushnell DA, Westover KD, Davis RE, Kornberg RD (February 2004). "Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms". Science. 303 (5660): 983–8. Bibcode:2004Sci...303..983B. doi:10.1126/science.1090838. PMID 14963322. S2CID 36598301.
  25. ↑ DeJong J, Bernstein R, Roeder RG (April 1995). "Human general transcription factor TFIIA: characterization of a cDNA encoding the small subunit and requirement for basal and activated transcription". Proc. Natl. Acad. Sci. U.S.A. 92 (8): 3313–7. Bibcode:1995PNAS...92.3313D. doi:10.1073/pnas.92.8.3313. PMC 42156. PMID 7724559.
  26. ↑ Ozer J, Mitsouras K, Zerby D, Carey M, Lieberman PM (June 1998). "Transcription factor IIA derepresses TATA-binding protein (TBP)-associated factor inhibition of TBP-DNA binding". J. Biol. Chem. 273 (23): 14293–300. doi:10.1074/jbc.273.23.14293. PMID 9603936.
  27. ↑ Sun X, Ma D, Sheldon M, Yeung K, Reinberg D (October 1994). "Reconstitution of human TFIIA activity from recombinant polypeptides: a role in TFIID-mediated transcription". Genes Dev. 8 (19): 2336–48. doi:10.1101/gad.8.19.2336. PMID 7958900.
  28. ↑ Ruppert S, Tjian R (November 1995). "Human TAFII250 interacts with RAP74: implications for RNA polymerase II initiation". Genes Dev. 9 (22): 2747–55. doi:10.1101/gad.9.22.2747. PMID 7590250.
  29. ↑ Malik S, Guermah M, Roeder RG (March 1998). "A dynamic model for PC4 coactivator function in RNA polymerase II transcription". Proc. Natl. Acad. Sci. U.S.A. 95 (5): 2192–7. Bibcode:1998PNAS...95.2192M. doi:10.1073/pnas.95.5.2192. PMC 19292. PMID 9482861.
  30. ↑ Thut CJ, Goodrich JA, Tjian R (August 1997). "Repression of p53-mediated transcription by MDM2: a dual mechanism". Genes Dev. 11 (15): 1974–86. doi:10.1101/gad.11.15.1974. PMC 316412. PMID 9271120.
  31. ↑ Léveillard T, Wasylyk B (December 1997). "The MDM2 C-terminal region binds to TAFII250 and is required for MDM2 regulation of the cyclin A promoter". J. Biol. Chem. 272 (49): 30651–61. doi:10.1074/jbc.272.49.30651. PMID 9388200.
  32. ↑ Shetty S, Takahashi T, Matsui H, Ayengar R, Raghow R (May 1999). "Transcriptional autorepression of Msx1 gene is mediated by interactions of Msx1 protein with a multi-protein transcriptional complex containing TATA-binding protein, Sp1 and cAMP-response-element-binding protein-binding protein (CBP/p300)". Biochem. J. 339 (3): 751–8. doi:10.1042/0264-6021:3390751. PMC 1220213. PMID 10215616.
  33. ↑ Zhang H, Hu G, Wang H, Sciavolino P, Iler N, Shen MM, Abate-Shen C (May 1997). "Heterodimerization of Msx and Dlx homeoproteins results in functional antagonism". Mol. Cell. Biol. 17 (5): 2920–32. doi:10.1128/mcb.17.5.2920. PMC 232144. PMID 9111364.
  34. ↑ Zhang H, Catron KM, Abate-Shen C (March 1996). "A role for the Msx-1 homeodomain in transcriptional regulation: residues in the N-terminal arm mediate TATA binding protein interaction and transcriptional repression". Proc. Natl. Acad. Sci. U.S.A. 93 (5): 1764–9. Bibcode:1996PNAS...93.1764Z. doi:10.1073/pnas.93.5.1764. PMC 39855. PMID 8700832.
  35. 1 2 3 4 5 6 7 8 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.
  36. ↑ Seto E, Usheva A, Zambetti GP, Momand J, Horikoshi N, Weinmann R, Levine AJ, Shenk T (December 1992). "Wild-type p53 binds to the TATA-binding protein and represses transcription". Proc. Natl. Acad. Sci. U.S.A. 89 (24): 12028–32. Bibcode:1992PNAS...8912028S. doi:10.1073/pnas.89.24.12028. PMC 50691. PMID 1465435.
  37. 1 2 Cvekl A, Kashanchi F, Brady JN, Piatigorsky J (June 1999). "Pax-6 interactions with TATA-box-binding protein and retinoblastoma protein". Invest. Ophthalmol. Vis. Sci. 40 (7): 1343–50. PMID 10359315.
  38. ↑ Zwilling S, Annweiler A, Wirth T (May 1994). "The POU domains of the Oct1 and Oct2 transcription factors mediate specific interaction with TBP". Nucleic Acids Res. 22 (9): 1655–62. doi:10.1093/nar/22.9.1655. PMC 308045. PMID 8202368.
  39. ↑ Guermah M, Malik S, Roeder RG (June 1998). "Involvement of TFIID and USA components in transcriptional activation of the human immunodeficiency virus promoter by NF-kappaB and Sp1". Mol. Cell. Biol. 18 (6): 3234–44. doi:10.1128/mcb.18.6.3234. PMC 108905. PMID 9584164.
  40. ↑ Schmitz ML, Stelzer G, Altmann H, Meisterernst M, Baeuerle PA (March 1995). "Interaction of the COOH-terminal transactivation domain of p65 NF-kappa B with TATA-binding protein, transcription factor IIB, and coactivators". J. Biol. Chem. 270 (13): 7219–26. doi:10.1074/jbc.270.13.7219. PMID 7706261.
  41. ↑ Schulman IG, Chakravarti D, Juguilon H, Romo A, Evans RM (August 1995). "Interactions between the retinoid X receptor and a conserved region of the TATA-binding protein mediate hormone-dependent transactivation". Proc. Natl. Acad. Sci. U.S.A. 92 (18): 8288–92. Bibcode:1995PNAS...92.8288S. doi:10.1073/pnas.92.18.8288. PMC 41142. PMID 7667283.
  42. ↑ Siegert JL, Robbins PD (January 1999). "Rb inhibits the intrinsic kinase activity of TATA-binding protein-associated factor TAFII250". Mol. Cell. Biol. 19 (1): 846–54. doi:10.1128/MCB.19.1.846. PMC 83941. PMID 9858607.
  43. 1 2 3 4 Ruppert S, Wang EH, Tjian R (March 1993). "Cloning and expression of human TAFII250: a TBP-associated factor implicated in cell-cycle regulation". Nature. 362 (6416): 175–9. Bibcode:1993Natur.362..175R. doi:10.1038/362175a0. PMID 7680771. S2CID 4364676.
  44. ↑ O'Brien T, Tjian R (May 1998). "Functional analysis of the human TAFII250 N-terminal kinase domain". Mol. Cell. 1 (6): 905–11. doi:10.1016/S1097-2765(00)80089-1. PMID 9660973.
  45. 1 2 3 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. S2CID 24519687.
  46. ↑ Tao Y, Guermah M, Martinez E, Oelgeschläger T, Hasegawa S, Takada R, Yamamoto T, Horikoshi M, Roeder RG (March 1997). "Specific interactions and potential functions of human TAFII100". J. Biol. Chem. 272 (10): 6714–21. doi:10.1074/jbc.272.10.6714. PMID 9045704.
  47. ↑ 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". Mol. Cell. Biol. 21 (20): 6782–95. doi:10.1128/MCB.21.20.6782-6795.2001. PMC 99856. PMID 11564863.
  48. 1 2 Mengus G, May M, Jacq X, Staub A, Tora L, Chambon P, Davidson I (April 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.
  49. ↑ 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.
  50. ↑ Hoffmann A, Roeder RG (July 1996). "Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation". J. Biol. Chem. 271 (30): 18194–202. doi:10.1074/jbc.271.30.18194. PMID 8663456.
  51. ↑ Hochheimer A, Tjian R (June 2003). "Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression". Genes & Development. 17 (11): 1309–20. doi:10.1101/gad.1099903. PMID 12782648.
  52. ↑ Pugh BF (September 2000). "Control of gene expression through regulation of the TATA-binding protein". Gene. 255 (1): 1–14. doi:10.1016/s0378-1119(00)00288-2. PMID 10974559.
  53. ↑ Weaver, Robert Franklin (1 January 2012). Molecular biology. McGraw-Hill. ISBN 9780073525327. OCLC 789601172.
  54. ↑ Louder RK, He Y, López-Blanco JR, Fang J, Chacón P, Nogales E (March 2016). "Structure of promoter-bound TFIID and model of human pre-initiation complex assembly". Nature. 531 (7596): 604–9. Bibcode:2016Natur.531..604L. doi:10.1038/nature17394. PMC 4856295. PMID 27007846.
  55. ↑ Davidson I (July 2003). "The genetics of TBP and TBP-related factors". Trends in Biochemical Sciences. 28 (7): 391–8. doi:10.1016/S0968-0004(03)00117-8. PMID 12878007.
  56. ↑ Nikolov DB, Hu SH, Lin J, Gasch A, Hoffmann A, Horikoshi M, Chua NH, Roeder RG, Burley SK (November 1992). "Crystal structure of TFIID TATA-box binding protein". Nature. 360 (6399): 40–6. Bibcode:1992Natur.360...40N. doi:10.1038/360040a0. PMID 1436073. S2CID 4307043.
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