1pft Citations

The N-terminal domain of TFIIB from Pyrococcus furiosus forms a zinc ribbon.

Nat Struct Biol 3 122-4 (1996)
Cited: 87 times
EuropePMC logo PMID: 8564536

Abstract

The three-dimensional structure of the N-terminal domain of an archaeal TFIIB, which has high sequence homology with eucaryal analogues, is strikingly similar to that of the C-terminal zinc ribbon of the eucaryal transcription elongation factor TFIIB.

Reviews - 1pft mentioned but not cited (2)

  1. Overview of protein structural and functional folds. Sun PD, Foster CE, Boyington JC. Curr Protoc Protein Sci Chapter 17 Unit 17.1 (2004)
  2. Host and Viral Zinc-Finger Proteins in COVID-19. Esposito S, D'Abrosca G, Antolak A, Pedone PV, Isernia C, Malgieri G. Int J Mol Sci 23 3711 (2022)

Articles - 1pft mentioned but not cited (6)

  1. Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome. Mochizuki T, Krupovic M, Pehau-Arnaudet G, Sako Y, Forterre P, Prangishvili D. Proc Natl Acad Sci U S A 109 13386-13391 (2012)
  2. Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain. Proudfoot M, Sanders SA, Singer A, Zhang R, Brown G, Binkowski A, Xu L, Lukin JA, Murzin AG, Joachimiak A, Arrowsmith CH, Edwards AM, Savchenko AV, Yakunin AF. J Mol Biol 375 301-315 (2008)
  3. Structure of the archaeal translation initiation factor aIF2 beta from Methanobacterium thermoautotrophicum: implications for translation initiation. Gutiérrez P, Osborne MJ, Siddiqui N, Trempe JF, Arrowsmith C, Gehring K. Protein Sci 13 659-667 (2004)
  4. Design of an optimal Chebyshev-expanded discrimination function for globular proteins. Fain B, Xia Y, Levitt M. Protein Sci 11 2010-2021 (2002)
  5. The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold. Herve du Penhoat C, Atreya HS, Shen Y, Liu G, Acton TB, Xiao R, Li Z, Murray D, Montelione GT, Szyperski T. Protein Sci 13 1407-1416 (2004)
  6. A conservation and rigidity based method for detecting critical protein residues. Akbal-Delibas B, Jagodzinski F, Haspel N. BMC Struct Biol 13 Suppl 1 S6 (2013)


Reviews citing this publication (20)

  1. Molecular genetics of the RNA polymerase II general transcriptional machinery. Hampsey M. Microbiol Mol Biol Rev 62 465-503 (1998)
  2. Structural basis of transcription initiation by RNA polymerase II. Sainsbury S, Bernecky C, Cramer P. Nat Rev Mol Cell Biol 16 129-143 (2015)
  3. The RNA polymerase II machinery: structure illuminates function. Woychik NA, Hampsey M. Cell 108 453-463 (2002)
  4. Mechanism and regulation of transcription in archaea. Bell SD, Jackson SP. Curr Opin Microbiol 4 208-213 (2001)
  5. Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features. Bell SD, Jackson SP. Trends Microbiol 6 222-228 (1998)
  6. Structural basis for sirtuin function: what we know and what we don't. Sanders BD, Jackson B, Marmorstein R. Biochim Biophys Acta 1804 1604-1616 (2010)
  7. Relationship between the architecture of zinc coordination and zinc binding affinity in proteins--insights into zinc regulation. Kochańczyk T, Drozd A, Krężel A. Metallomics 7 244-257 (2015)
  8. Transcription initiation in Archaea: facts, factors and future aspects. Soppa J. Mol Microbiol 31 1295-1305 (1999)
  9. Eukaryotic transcription factor-DNA complexes. Patikoglou G, Burley SK. Annu Rev Biophys Biomol Struct 26 289-325 (1997)
  10. TFIIB and the regulation of transcription by RNA polymerase II. Deng W, Roberts SG. Chromosoma 116 417-429 (2007)
  11. Structure of histone deacetylases: insights into substrate recognition and catalysis. Marmorstein R. Structure 9 1127-1133 (2001)
  12. Type IA topoisomerases: a simple puzzle? Viard T, de la Tour CB. Biochimie 89 456-467 (2007)
  13. Archaeal RNA polymerase and transcription regulation. Jun SH, Reichlen MJ, Tajiri M, Murakami KS. Crit Rev Biochem Mol Biol 46 27-40 (2011)
  14. Determinants of transcription initiation by archaeal RNA polymerase. Bartlett MS. Curr Opin Microbiol 8 677-684 (2005)
  15. The RNA polymerase II general transcription factors: past, present, and future. Reinberg D, Orphanides G, Ebright R, Akoulitchev S, Carcamo J, Cho H, Cortes P, Drapkin R, Flores O, Ha I, Inostroza JA, Kim S, Kim TK, Kumar P, Lagrange T, LeRoy G, Lu H, Ma DM, Maldonado E, Merino A, Mermelstein F, Olave I, Sheldon M, Shiekhattar R, Zawel L. Cold Spring Harb Symp Quant Biol 63 83-103 (1998)
  16. Transcription in Archaea. Bell SD, Jackson SP. Cold Spring Harb Symp Quant Biol 63 41-51 (1998)
  17. Transcriptional regulation in Archaea. Ouhammouch M. Curr Opin Genet Dev 14 133-138 (2004)
  18. Fractions to functions: RNA polymerase II thirty years later. Woychik NA. Cold Spring Harb Symp Quant Biol 63 311-317 (1998)
  19. Development and function of central cell in angiosperm female gametophyte. Liu Y, Yan Z, Chen N, Di X, Huang J, Guo G. Genesis 48 466-478 (2010)
  20. Transcription: building an initiation machine. Travers A. Curr Biol 6 401-403 (1996)

Articles citing this publication (59)

  1. Structural classification of zinc fingers: survey and summary. Krishna SS, Majumdar I, Grishin NV. Nucleic Acids Res 31 532-550 (2003)
  2. RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Kostrewa D, Zeller ME, Armache KJ, Seizl M, Leike K, Thomm M, Cramer P. Nature 462 323-330 (2009)
  3. Crystal structure of a SIR2 homolog-NAD complex. Min J, Landry J, Sternglanz R, Xu RM. Cell 105 269-279 (2001)
  4. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Nunokawa E, Ishizuka Y, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S. J Mol Biol 337 49-63 (2004)
  5. RNA polymerase II transcription initiation: a structural view. Nikolov DB, Burley SK. Proc Natl Acad Sci U S A 94 15-22 (1997)
  6. The central cell plays a critical role in pollen tube guidance in Arabidopsis. Chen YH, Li HJ, Shi DQ, Yuan L, Liu J, Sreenivasan R, Baskar R, Grossniklaus U, Yang WC. Plant Cell 19 3563-3577 (2007)
  7. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Chen HT, Hahn S. Cell 119 169-180 (2004)
  8. Different human TFIIIB activities direct RNA polymerase III transcription from TATA-containing and TATA-less promoters. Schramm L, Pendergrast PS, Sun Y, Hernandez N. Genes Dev 14 2650-2663 (2000)
  9. Binding of TFIIB to RNA polymerase II: Mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex. Chen HT, Hahn S. Mol Cell 12 437-447 (2003)
  10. High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex. Lagrange T, Kim TK, Orphanides G, Ebright YW, Ebright RH, Reinberg D. Proc Natl Acad Sci U S A 93 10620-10625 (1996)
  11. Mutational analysis of yeast TFIIB. A functional relationship between Ssu72 and Sub1/Tsp1 defined by allele-specific interactions with TFIIB. Wu WH, Pinto I, Chen BS, Hampsey M. Genetics 153 643-652 (1999)
  12. Solution structure of the cysteine-rich domain of the Escherichia coli chaperone protein DnaJ. Martinez-Yamout M, Legge GB, Zhang O, Wright PE, Dyson HJ. J Mol Biol 300 805-818 (2000)
  13. Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase. Pan H, Wigley DB. Structure 8 231-239 (2000)
  14. Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface. Okuda M, Watanabe Y, Okamura H, Hanaoka F, Ohkuma Y, Nishimura Y. EMBO J 19 1346-1356 (2000)
  15. A human RNA viral cysteine proteinase that depends upon a unique Zn2+-binding finger connecting the two domains of a papain-like fold . Herold J, Siddell SG, Gorbalenya AE. J Biol Chem 274 14918-14925 (1999)
  16. The role of transcription factor B in transcription initiation and promoter clearance in the archaeon Sulfolobus acidocaldarius. Bell SD, Jackson SP. J Biol Chem 275 12934-12940 (2000)
  17. The Cys4 zinc finger of bacteriophage T7 primase in sequence-specific single-stranded DNA recognition. Kusakabe T, Hine AV, Hyberts SG, Richardson CC. Proc Natl Acad Sci U S A 96 4295-4300 (1999)
  18. Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription. Chen HT, Legault P, Glushka J, Omichinski JG, Scott RA. Protein Sci 9 1743-1752 (2000)
  19. Architecture of protein and DNA contacts within the TFIIIB-DNA complex. Colbert T, Lee S, Schimmack G, Hahn S. Mol Cell Biol 18 1682-1691 (1998)
  20. Genetic analysis of the large subunit of yeast transcription factor IIE reveals two regions with distinct functions. Kuldell NH, Buratowski S. Mol Cell Biol 17 5288-5298 (1997)
  21. High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases. Wang B, Jones DN, Kaine BP, Weiss MA. Structure 6 555-569 (1998)
  22. C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily. Grishin NV. J Mol Biol 299 1165-1177 (2000)
  23. The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation. Hahn S, Roberts S. Genes Dev 14 719-730 (2000)
  24. Mutational analysis of the D1/E1 core helices and the conserved N-terminal region of yeast transcription factor IIB (TFIIB): identification of an N-terminal mutant that stabilizes TATA-binding protein-TFIIB-DNA complexes. Bangur CS, Pardee TS, Ponticelli AS. Mol Cell Biol 17 6784-6793 (1997)
  25. An activation-specific role for transcription factor TFIIB in vivo. Wu WH, Hampsey M. Proc Natl Acad Sci U S A 96 2764-2769 (1999)
  26. Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex. Freire-Picos MA, Krishnamurthy S, Sun ZW, Hampsey M. Nucleic Acids Res 33 5045-5052 (2005)
  27. Functional interaction between TFIIB and the Rpb2 subunit of RNA polymerase II: implications for the mechanism of transcription initiation. Chen BS, Hampsey M. Mol Cell Biol 24 3983-3991 (2004)
  28. The solution structure of ribosomal protein L36 from Thermus thermophilus reveals a zinc-ribbon-like fold. Härd T, Rak A, Allard P, Kloo L, Garber M. J Mol Biol 296 169-180 (2000)
  29. Core promoter-dependent TFIIB conformation and a role for TFIIB conformation in transcription start site selection. Fairley JA, Evans R, Hawkes NA, Roberts SG. Mol Cell Biol 22 6697-6705 (2002)
  30. Crystal structure of full length topoisomerase I from Thermotoga maritima. Hansen G, Harrenga A, Wieland B, Schomburg D, Reinemer P. J Mol Biol 358 1328-1340 (2006)
  31. The crenarchaeal DNA damage-inducible transcription factor B paralogue TFB3 is a general activator of transcription. Paytubi S, White MF. Mol Microbiol 72 1487-1499 (2009)
  32. A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase. Logan DT, Mulliez E, Larsson KM, Bodevin S, Atta M, Garnaud PE, Sjoberg BM, Fontecave M. Proc Natl Acad Sci U S A 100 3826-3831 (2003)
  33. Structure-function analysis of the human TFIIB-related factor II protein reveals an essential role for the C-terminal domain in RNA polymerase III transcription. Saxena A, Ma B, Schramm L, Hernandez N. Mol Cell Biol 25 9406-9418 (2005)
  34. A conformational change in TFIIB is required for activator-mediated assembly of the preinitiation complex. Glossop JA, Dafforn TR, Roberts SG. Nucleic Acids Res 32 1829-1835 (2004)
  35. Assembly of transcription factor IIB at a promoter in vivo requires contact with RNA polymerase II. Elsby LM, O'Donnell AJ, Green LM, Sharrocks AD, Roberts SG. EMBO Rep 7 898-903 (2006)
  36. Elongation factor TFIIS contains three structural domains: solution structure of domain II. Morin PE, Awrey DE, Edwards AM, Arrowsmith CH. Proc Natl Acad Sci U S A 93 10604-10608 (1996)
  37. Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response. Schult F, Le TN, Albersmeier A, Rauch B, Blumenkamp P, van der Does C, Goesmann A, Kalinowski J, Albers SV, Siebers B. Nucleic Acids Res 46 7179-7192 (2018)
  38. Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei. Ibrahim BS, Kanneganti N, Rieckhof GE, Das A, Laurents DV, Palenchar JB, Bellofatto V, Wah DA. Proc Natl Acad Sci U S A 106 13242-13247 (2009)
  39. A new zinc ribbon gene (ZNRD1) is cloned from the human MHC class I region. Fan W, Wang Z, Kyzysztof F, Prange C, Lennon G. Genomics 63 139-141 (2000)
  40. A structural tree for proteins containing 3beta-corners. Efimov AV. FEBS Lett 407 37-41 (1997)
  41. Nuclear import of TFIIB is mediated by Kap114p, a karyopherin with multiple cargo-binding domains. Hodges JL, Leslie JH, Mosammaparast N, Guo Y, Shabanowitz J, Hunt DF, Pemberton LF. Mol Biol Cell 16 3200-3210 (2005)
  42. A structural tree for proteins containing S-like beta-sheets. Efimov AV. FEBS Lett 437 246-250 (1998)
  43. Isolation of TBP-interacting protein (TIP) from a hyperthermophilic archaeon that inhibits the binding of TBP to TATA-DNA. Matsuda T, Morikawa M, Haruki M, Higashibata H, Imanaka T, Kanaya S. FEBS Lett 457 38-42 (1999)
  44. Transcription of bacteriophage PM2 involves phage-encoded regulators of heterologous origin. Männistö RH, Grahn AM, Bamford DH, Bamford JK. J Bacteriol 185 3278-3287 (2003)
  45. DNA inhibits catalysis by the carboxyltransferase subunit of acetyl-CoA carboxylase: implications for active site communication. Benson BK, Meades G, Grove A, Waldrop GL. Protein Sci 17 34-42 (2008)
  46. Functional analysis of archaeal MBF1 by complementation studies in yeast. Marrero Coto J, Ehrenhofer-Murray AE, Pons T, Siebers B. Biol Direct 6 18 (2011)
  47. Mercury inactivates transcription and the generalized transcription factor TFB in the archaeon Sulfolobus solfataricus. Dixit V, Bini E, Drozda M, Blum P. Antimicrob Agents Chemother 48 1993-1999 (2004)
  48. Interdependent interactions between TFIIB, TATA binding protein, and DNA. Buratowski RM, Downs J, Buratowski S. Mol Cell Biol 22 8735-8743 (2002)
  49. Intramolecular interaction of yeast TFIIB in transcription control. Zhang DY, Dorsey MJ, Voth WP, Carson DJ, Zeng X, Stillman DJ, Ma J. Nucleic Acids Res 28 1913-1920 (2000)
  50. Mutational studies of yeast transcription factor IIB in vivo reveal a functional surface important for gene activation. Shaw SP, Carson DJ, Dorsey MJ, Ma J. Proc Natl Acad Sci U S A 94 2427-2432 (1997)
  51. Model of the TBP-TFIIB complex from Plasmodium falciparum: interface analysis and perspectives as a new target for antimalarial design. Buendía-Orozco J, Guerrero A, Pastor N. Arch Med Res 36 317-330 (2005)
  52. RNA polymerase subunit H features a beta-ribbon motif within a novel fold that is present in archaea and eukaryotes. Thiru A, Hodach M, Eloranta JJ, Kostourou V, Weinzierl RO, Matthews S. J Mol Biol 287 753-760 (1999)
  53. Solution structure of ribosomal protein L40E, a unique C4 zinc finger protein encoded by archaeon Sulfolobus solfataricus. Wu B, Lukin J, Yee A, Lemak A, Semesi A, Ramelot TA, Kennedy MA, Arrowsmith CH. Protein Sci 17 589-596 (2008)
  54. Identification of a putative BRF homologue in the genome of Caenorhabditis elegans. Larminie CG, White RJ. DNA Seq 9 49-58 (1998)
  55. Hypomutable regions of yeast TFIIB in a unigenic evolution test represent structural domains. Zeng X, Zhang D, Dorsey M, Ma J. Gene 309 49-56 (2003)
  56. Role of the inhibitory DNA-binding surface of human TATA-binding protein in recruitment of human TFIIB family members. Zhao X, Herr W. Mol Cell Biol 23 8152-8160 (2003)
  57. Structural insights into the asymmetric effects of zinc-ligand cysteine mutations in the novel zinc ribbon domain of human TFIIEalpha for transcription. Okuda M, Tanaka A, Hanaoka F, Ohkuma Y, Nishimura Y. J Biochem 138 443-449 (2005)
  58. Letter The core histone fold: limits to functional versatility. Ouzounis CA, Kyrpides NC. J Mol Evol 43 541-542 (1996)
  59. Aromatic Ring Currents at a Protein Surface: Use of (1)H-NMR Chemical Shifts to Refine the Structure of a Naked β Sheet. Wang B, Stern AS, Weiss MA. J Biomol Struct Dyn 17 Suppl 1 95-108 (2000)