spacer
spacer
Go to PDB code: 
protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
1ais
Jmol
Contents
Protein chains
181 a.a. *
193 a.a. *
DNA/RNA
Waters ×288
* Residue conservation analysis
PDB id:
1ais
Name: Transcription/DNA
Title: Tata-binding protein/transcription factor (ii)b/tata-box complex from pyrococcus woesei
Structure: DNA (5'-d( Ap Ap Cp Tp Tp Ap Cp Tp Tp Tp (5Iu) p (5Iu)p Ap Ap Ap Gp C)-3'). Chain: c. Engineered: yes. DNA (5'- d( Gp Cp Tp Tp Tp Ap Ap Ap Ap Ap Gp Tp Ap Ap Gp Tp T )-3'). Chain: e. Engineered: yes. Protein (tata-binding protein).
Source: Synthetic: yes. Pyrococcus woesei. Organism_taxid: 2262. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: de3.
Biol. unit: Tetramer (from PQS)
Resolution:
2.10Å     R-factor:   0.212     R-free:   0.268
Authors: P.F.Kosa,G.Ghosh,B.S.Dedecker,P.B.Sigler
Key ref:
P.F.Kosa et al. (1997). The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box. Proc Natl Acad Sci U S A, 94, 6042-6047. PubMed id: 9177165 DOI: 10.1073/pnas.94.12.6042
Date:
24-Apr-97     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62001  (TBP_PYRWO) -  TATA-box-binding protein
Seq:
Struc: 		191 a.a.
181 a.a.
Protein chain
Pfam   ArchSchema ?
P61999  (TF2B_PYRWO) -  Transcription initiation factor IIB
Seq:
Struc: 		300 a.a.
193 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription   6 terms 
  Biochemical function     binding     7 terms  

 

 
DOI no: 10.1073/pnas.94.12.6042 Proc Natl Acad Sci U S A 94:6042-6047 (1997)
PubMed id: 9177165  
 
 
The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box.
P.F.Kosa, G.Ghosh, B.S.DeDecker, P.B.Sigler.
 
  ABSTRACT  
 
Archaea possess a basal transcriptional apparatus that resembles that of eukaryotes. Here we report the 2.1-A crystal structure of the archaeal transcription factor complex formed by the TATA-box-binding protein (TBP), the transcription factor IIB homolog, and a DNA target, all from the hyperthermophile Pyrococcus woesei. The overall fold of these two basal transcription factors is essentially the same as that of their eukaryotic counterparts. However, in comparison with the eukaryotic complexes, the archaeal TBP-DNA interface is more symmetrical, and in this structure the orientation of the preinitiation complex assembly on the promoter is inverted with respect to that seen in all crystal structures of comparable eukaryotic systems. This study of the structural details of an archaeal transcription factor complex presents the opportunity to examine the evolution of the basal eukaryotic transcriptional apparatus from a stereochemical viewpoint and to extend our understanding of the physical biochemistry of transcriptional initiation.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereo pair of electron density of a sigma A weighted (26) 2|F[o]| |F[c]| map, contoured at 2 . pwTFB[c] residues are magenta, pwTBP residues are white, DNA is yellow, and water molecules are^ orange spheres. 		Figure 3.
Fig. 3. (a) Ribbons (28) drawing of the overall structure of the ternary complex. pwTBP is in red, the N-terminal domain of pwTFB[c]^ is green, the C-terminal domain is yellow, and DNA is blue. (b) Stereo drawing of pwTFB[c], with the same orientation as in a.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21250781 S.H.Jun, M.J.Reichlen, M.Tajiri, and K.S.Murakami (2011).
Archaeal RNA polymerase and transcription regulation.
  Crit Rev Biochem Mol Biol, 46, 27-40.  
21502537 S.Liu, M.Balasov, H.Wang, L.Wu, I.N.Chesnokov, and Y.Liu (2011).
Structural analysis of human Orc6 protein reveals a homology with transcription factor TFIIB.
  Proc Natl Acad Sci U S A, 108, 7373-7378.
PDB code: 3m03
  21326901 S.De Carlo, S.C.Lin, D.J.Taatjes, and A.Hoenger (2010).
Molecular basis of transcription initiation in Archaea.
  Transcr, 1, 103-111.  
19666603 B.S.Ibrahim, N.Kanneganti, G.E.Rieckhof, A.Das, D.V.Laurents, J.B.Palenchar, V.Bellofatto, and D.A.Wah (2009).
Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei.
  Proc Natl Acad Sci U S A, 106, 13242-13247.
PDB code: 3h4c
19359364 J.Zhang, E.Li, and G.J.Olsen (2009).
Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii.
  Nucleic Acids Res, 37, 3588-3601.  
19007415 M.Ouhammouch, W.Hausner, and E.P.Geiduschek (2009).
TBP domain symmetry in basal and activated archaeal transcription.
  Mol Microbiol, 71, 123-131.  
19668860 S.Nagatoishi, Y.Tanaka, M.Kudou, and K.Tsumoto (2009).
The interaction of hyperthermophilic TATA-box binding protein with single-stranded DNA is entropically favorable and exhibits a large negative heat capacity change at high salt concentration.
  Mol Biosyst, 5, 957-961.  
19228197 T.Tadokoro, and S.Kanaya (2009).
Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes.
  FEBS J, 276, 1482-1493.  
18981048 E.Li, C.I.Reich, and G.J.Olsen (2008).
A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii.
  Nucleic Acids Res, 36, 6948-6958.  
18326635 J.H.Bredenberg, C.Russo, and M.O.Fenley (2008).
Salt-mediated electrostatics in the association of TATA binding proteins to DNA: a combined molecular mechanics/Poisson-Boltzmann study.
  Biophys J, 94, 4634-4645.  
18056077 M.Bauer, L.Marschaus, M.Reuff, V.Besche, S.Sartorius-Neef, and F.Pfeifer (2008).
Overlapping activator sequences determined for two oppositely oriented promoters in halophilic Archaea.
  Nucleic Acids Res, 36, 598-606.  
18159946 M.Brenneis, O.Hering, C.Lange, and J.Soppa (2007).
Experimental characterization of Cis-acting elements important for translation and transcription in halophilic archaea.
  PLoS Genet, 3, e229.  
17275836 T.J.Santangelo, L.Cubonová, C.L.James, and J.N.Reeve (2007).
TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro.
  J Mol Biol, 367, 344-357.  
16531230 N.Tochio, T.Umehara, S.Koshiba, M.Inoue, T.Yabuki, M.Aoki, E.Seki, S.Watanabe, Y.Tomo, M.Hanada, M.Ikari, M.Sato, T.Terada, T.Nagase, O.Ohara, M.Shirouzu, A.Tanaka, T.Kigawa, and S.Yokoyama (2006).
Solution structure of the SWIRM domain of human histone demethylase LSD1.
  Structure, 14, 457-468.
PDB code: 2com
16391031 S.V.Albers, M.Jonuscheit, S.Dinkelaker, T.Urich, A.Kletzin, R.Tampé, A.J.Driessen, and C.Schleper (2006).
Production of recombinant and tagged proteins in the hyperthermophilic archaeon Sulfolobus solfataricus.
  Appl Environ Microbiol, 72, 102-111.  
16322571 T.Yamamoto, T.Matsuda, T.Inoue, H.Matsumura, M.Morikawa, S.Kanaya, and Y.Kai (2006).
Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA.
  Protein Sci, 15, 152-161.
PDB code: 2czr
16230629 M.Ouhammouch, and E.P.Geiduschek (2005).
An expanding family of archaeal transcriptional activators.
  Proc Natl Acad Sci U S A, 102, 15423-15428.  
14872062 D.J.Richard, S.D.Bell, and M.F.White (2004).
Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase.
  Nucleic Acids Res, 32, 1065-1074.  
15614969 N.Adachi, R.Natsume, M.Senda, S.Muto, T.Senda, and M.Horikoshi (2004).
Purification, crystallization and preliminary X-ray analysis of Methanococcus jannaschii TATA box-binding protein (TBP).
  Acta Crystallogr D Biol Crystallogr, 60, 2328-2331.  
15155190 V.Dixit, E.Bini, M.Drozda, and P.Blum (2004).
Mercury inactivates transcription and the generalized transcription factor TFB in the archaeon Sulfolobus solfataricus.
  Antimicrob Agents Chemother, 48, 1993-1999.  
14536083 H.T.Chen, and S.Hahn (2003).
Binding of TFIIB to RNA polymerase II: Mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex.
  Mol Cell, 12, 437-447.  
12446791 J.V.Spencer, and K.M.Arndt (2002).
A TATA binding protein mutant with increased affinity for DNA directs transcription from a reversed TATA sequence in vivo.
  Mol Cell Biol, 22, 8744-8755.  
  12015146 S.Bergqvist, M.A.Williams, R.O'Brien, and J.E.Ladbury (2002).
Reversal of halophilicity in a protein-DNA interaction by limited mutation strategy.
  Structure, 10, 629-637.  
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
  Nucleic Acids Res, 30, 1182-1191.  
11461703 K.Kamada, F.Shu, H.Chen, S.Malik, G.Stelzer, R.G.Roeder, M.Meisterernst, and S.K.Burley (2001).
Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex.
  Cell, 106, 71-81.
PDB code: 1jfi
11327862 S.Bergqvist, R.O'Brien, and J.E.Ladbury (2001).
Site-specific cation binding mediates TATA binding protein-DNA interaction from a hyperthermophilic archaeon.
  Biochemistry, 40, 2419-2425.  
11258705 S.D.Bell, A.B.Brinkman, J.van der Oost, and S.P.Jackson (2001).
The archaeal TFIIEalpha homologue facilitates transcription initiation by enhancing TATA-box recognition.
  EMBO Rep, 2, 133-138.  
  11282478 S.D.Bell, and S.P.Jackson (2001).
Mechanism and regulation of transcription in archaea.
  Curr Opin Microbiol, 4, 208-213.  
11591641 S.P.Kennedy, W.V.Ng, S.L.Salzberg, L.Hood, and S.DasSarma (2001).
Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence.
  Genome Res, 11, 1641-1650.  
10619841 F.T.Tsai, and P.B.Sigler (2000).
Structural basis of preinitiation complex assembly on human pol II promoters.
  EMBO J, 19, 25-36.
PDB code: 1c9b
11754342 I.Lafontaine, and R.Lavery (2000).
ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences.
  Biopolymers, 56, 292-310.  
10733977 L.Pardo, M.Campillo, D.Bosch, N.Pastor, and H.Weinstein (2000).
Binding mechanisms of TATA box-binding proteins: DNA kinking is stabilized by specific hydrogen bonds.
  Biophys J, 78, 1988-1996.  
10027980 A.Hochheimer, R.Hedderich, and R.K.Thauer (1999).
The DNA binding protein Tfx from Methanobacterium thermoautotrophicum: structure, DNA binding properties and transcriptional regulation.
  Mol Microbiol, 31, 641-650.  
10476041 D.K.Thompson, J.R.Palmer, and C.J.Daniels (1999).
Expression and heat-responsive regulation of a TFIIB homologue from the archaeon Haloferax volcanii.
  Mol Microbiol, 33, 1081-1092.  
10617571 G.A.Patikoglou, J.L.Kim, L.Sun, S.H.Yang, T.Kodadek, and S.K.Burley (1999).
TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.
  Genes Dev, 13, 3217-3230.
PDB codes: 1qn3 1qn4 1qn5 1qn6 1qn7 1qn8 1qn9 1qna 1qnb 1qnc 1qne
10470030 J.C.Dantonel, J.M.Wurtz, O.Poch, D.Moras, and L.Tora (1999).
The TBP-like factor: an alternative transcription factor in metazoa?
  Trends Biochem Sci, 24, 335-339.  
  10373570 J.Persinger, S.M.Sengupta, and B.Bartholomew (1999).
Spatial organization of the core region of yeast TFIIIB-DNA complexes.
  Mol Cell Biol, 19, 5218-5234.  
10200952 J.Soppa (1999).
Transcription initiation in Archaea: facts, factors and future aspects.
  Mol Microbiol, 31, 1295-1305.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10570130 O.Littlefield, Y.Korkhin, and P.B.Sigler (1999).
The structural basis for the oriented assembly of a TBP/TFB/promoter complex.
  Proc Natl Acad Sci U S A, 96, 13668-13673.
PDB code: 1d3u
9919650 R.Cannio, G.Fiorentino, M.Rossi, and S.Bartolucci (1999).
The alcohol dehydrogenase gene: distribution among Sulfolobales and regulation in Sulfolobus solfataricus.
  FEMS Microbiol Lett, 170, 31-39.  
10570129 S.D.Bell, P.L.Kosa, P.B.Sigler, and S.P.Jackson (1999).
Orientation of the transcription preinitiation complex in archaea.
  Proc Natl Acad Sci U S A, 96, 13662-13667.  
10635322 S.D.Bell, S.S.Cairns, R.L.Robson, and S.P.Jackson (1999).
Transcriptional regulation of an archaeal operon in vivo and in vitro.
  Mol Cell, 4, 971-982.  
9399877 A.D.Baxevanis, and D.Landsman (1998).
Histone Sequence Database: new histone fold family members.
  Nucleic Acids Res, 26, 372-375.  
9646864 C.A.Bewley, A.M.Gronenborn, and G.M.Clore (1998).
Minor groove-binding architectural proteins: structure, function, and DNA recognition.
  Annu Rev Biophys Biomol Struct, 27, 105-131.  
9489666 D.K.Thompson, and C.J.Daniels (1998).
Heat shock inducibility of an archaeal TATA-like promoter is controlled by adjacent sequence elements.
  Mol Microbiol, 27, 541-551.  
9741622 D.Liu, R.Ishima, K.I.Tong, S.Bagby, T.Kokubo, D.R.Muhandiram, L.E.Kay, Y.Nakatani, and M.Ikura (1998).
Solution structure of a TBP-TAF(II)230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP.
  Cell, 94, 573-583.
PDB code: 1tba
9628480 D.N.Arvidson, F.Lu, C.Faber, H.Zalkin, and R.G.Brennan (1998).
The structure of PurR mutant L54M shows an alternative route to DNA kinking.
  Nat Struct Biol, 5, 436-441.
PDB code: 1vpw
9609687 F.Hayashi, R.Ishima, D.Liu, K.I.Tong, S.Kim, D.Reinberg, S.Bagby, and M.Ikura (1998).
Human general transcription factor TFIIB: conformational variability and interaction with VP16 activation domain.
  Biochemistry, 37, 7941-7951.
PDB code: 1tfb
10384270 F.T.Tsai, O.Littlefield, P.F.Kosa, J.M.Cox, A.Schepartz, and P.B.Sigler (1998).
Polarity of transcription on Pol II and archaeal promoters: where is the "one-way sign" and how is it read?
  Cold Spring Harb Symp Quant Biol, 63, 53-61.  
  9667920 J.M.Cox, A.R.Kays, J.F.Sanchez, and A.Schepartz (1998).
Preinitation complex assembly: potentially a bumpy path.
  Curr Opin Chem Biol, 2, 11-17.  
9591646 L.Pardo, N.Pastor, and H.Weinstein (1998).
Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond.
  Biophys J, 74, 2191-2198.  
9788936 L.Pardo, N.Pastor, and H.Weinstein (1998).
Selective binding of the TATA box-binding protein to the TATA box-containing promoter: analysis of structural and energetic factors.
  Biophys J, 75, 2411-2421.  
9860949 S.D.Bell, C.Jaxel, M.Nadal, P.F.Kosa, and S.P.Jackson (1998).
Temperature, template topology, and factor requirements of archaeal transcription.
  Proc Natl Acad Sci U S A, 95, 15218-15222.  
10384269 S.D.Bell, and S.P.Jackson (1998).
Transcription in Archaea.
  Cold Spring Harb Symp Quant Biol, 63, 41-51.  
  9675798 S.D.Bell, and S.P.Jackson (1998).
Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features.
  Trends Microbiol, 6, 222-228.  
9519295 S.Tan, and T.J.Richmond (1998).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 8, 41-48.  
  9488485 T.Colbert, S.Lee, G.Schimmack, and S.Hahn (1998).
Architecture of protein and DNA contacts within the TFIIIB-DNA complex.
  Mol Cell Biol, 18, 1682-1691.  
  9420329 T.Lagrange, A.N.Kapanidis, H.Tang, D.Reinberg, and R.H.Ebright (1998).
New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB.
  Genes Dev, 12, 34-44.  
9363785 J.Soppa, and T.A.Link (1997).
The TATA-box-binding protein (TBP) of Halobacterium salinarum. Cloning of the tbp gene, heterologous production of TBP and folding of TBP into a native conformation.
  Eur J Biochem, 249, 318-324.  
9782775 M.Tateno, K.Yamasaki, N.Amano, J.Kakinuma, H.Koike, M.D.Allen, and M.Suzuki (1997).
DNA recognition by beta-sheets.
  Biopolymers, 44, 335-359.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.