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PDBsum entry 1l9z

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protein dna_rna metals Protein-protein interface(s) links
Transcription/DNA PDB id
1l9z
Jmol
Contents
Protein chains
224 a.a. *
1084 a.a. *
1183 a.a. *
92 a.a. *
319 a.a. *
DNA/RNA
Metals
_ZN ×2
_MG
* Residue conservation analysis
PDB id:
1l9z
Name: Transcription/DNA
Title: Thermus aquaticus RNA polymerase holoenzyme/fork-junction promoter DNA complex at 6.5 a resolution
Structure: Nontemplate DNA strand. Chain: u. Engineered: yes. Template DNA strand. Chain: t. Engineered: yes. RNA polymerase, alpha subunit. Chain: a, b. RNA polymerase, beta subunit.
Source: Synthetic: yes. Thermus aquaticus. Organism_taxid: 271. Gene: rpod. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Octamer (from PQS)
Resolution:
6.50Å     R-factor:   not given    
Authors: K.S.Murakami,S.Masuda,E.A.Campbell,O.Muzzin,S.A.Darst
Key ref:
K.S.Murakami et al. (2002). Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science, 296, 1285-1290. PubMed id: 12016307 DOI: 10.1126/science.1069595
Date:
27-Mar-02     Release date:   31-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9KWU8  (RPOA_THEAQ) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
314 a.a.
224 a.a.
Protein chain
Pfam   ArchSchema ?
Q9KWU7  (RPOB_THEAQ) -  DNA-directed RNA polymerase subunit beta
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1119 a.a.
1084 a.a.
Protein chain
Pfam   ArchSchema ?
Q9KWU6  (RPOC_THEAQ) -  DNA-directed RNA polymerase subunit beta'
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1524 a.a.
1183 a.a.
Protein chain
Pfam   ArchSchema ?
Q9EVV4  (RPOZ_THEAQ) -  DNA-directed RNA polymerase subunit omega
Seq:
Struc:
99 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
Q9EZJ8  (Q9EZJ8_THEAQ) -  RNA polymerase sigma factor SigA
Seq:
Struc:
438 a.a.
319 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     transcription initiation from bacterial-type RNA polymerase promoter   6 terms 
  Biochemical function     transferase activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.1069595 Science 296:1285-1290 (2002)
PubMed id: 12016307  
 
 
Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.
K.S.Murakami, S.Masuda, E.A.Campbell, O.Muzzin, S.A.Darst.
 
  ABSTRACT  
 
The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha2betabeta'omegasigmaA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the sigma subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the sigma subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Fork-junction DNA and electron density map. (A) Synthetic DNA oligonucleotides used for complex formation and crystallization. The numbers above denote the DNA position with respect to the transcription start site at +1. Downstream corresponds to the direction of RNAP movement during transcription. Mutations in the bottom DNA strand cause corresponding mutations in the RNA transcript, defining it as the template (versus the nontemplate) strand. The DNA sequence is derived from the full con promoter (4), with -35 and -10 elements (shaded yellow and labeled) as well as an extended -10 element (shaded red and labeled). (B) Stereo view of the Taq RNAP holoenzyme/fork-junction DNA complex. The -carbon backbone of is colored white, cyan, ' pink, and orange (the subunits are not visible). The DNA template strand is colored dark green, and the nontemplate strand is light green, except for the -35 and -10 elements, which are colored yellow. The visible structural domains of ( [2] and [4]) (1, 9) are labeled. The direction of transcription (downstream) is to the right. The experimental electron density map, calculated using observed amplitude (F[o]) coefficients, is shown (blue net, contoured at 1.5 ), and was computed using multiple isomorphous replacement phases (Table 1), followed by density modification. The view is sliced at a level just in front of the DNA to reveal the ' NH[2]-terminal Zn2+-binding domain and the associated Zn2+ (labeled, shown as a green sphere). Shown in red is a difference Fourier map, calculated using (|F[o]EMTS - F[o]native|) coefficients (Table 1), revealing the Hg-binding site that was used to locate the Zn2+-site.
Figure 3.
Fig. 3. Conformational changes. The superimposed -carbon backbones of the Taq RNAP holoenzyme alone (1) and the holoenzyme within the fork-junction DNA complex are shown as worms (view the same as Fig. 2A). The structure of holoenzyme alone is colored gray (core RNAP) and black ( ). The two modules that move in the holoenzyme-DNA complex as compared with the holoenzyme alone are colored as follows: clamp + [2], magenta and orange (respectively); flap + [4], blue and orange (respectively). The phosphate backbones of the DNA in the holoenzyme/DNA complex are shown as ribbons and colored green (template strand, t) and light green (nontemplate strand, nt). The downstream direction is indicated. The movements of the mobile modules from the holoenzyme structure to their positions in the holoenzyme-DNA complex are indicated by the arrows.
 
  The above figures are reprinted by permission from the AAAs: Science (2002, 296, 1285-1290) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21316373 C.Sheppard, B.Cámara, A.Shadrin, N.Akulenko, M.Liu, G.Baldwin, K.Severinov, E.Cota, S.Matthews, and S.R.Wigneshweraraj (2011).
Inhibition of Escherichia coli RNAp by T7 Gp2 protein: role of negatively charged strip of amino acid residues in Gp2.
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21386817 F.W.Martinez-Rucobo, S.Sainsbury, A.C.Cheung, and P.Cramer (2011).
Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity.
  EMBO J, 30, 1302-1310.
PDB code: 3qqc
21233849 F.Werner, and D.Grohmann (2011).
Evolution of multisubunit RNA polymerases in the three domains of life.
  Nat Rev Microbiol, 9, 85-98.  
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.  
20562828 A.Tupin, M.Gualtieri, J.P.Leonetti, and K.Brodolin (2010).
The transcription inhibitor lipiarmycin blocks DNA fitting into the RNA polymerase catalytic site.
  EMBO J, 29, 2527-2537.  
  21029433 D.M.Hinton (2010).
Transcriptional control in the prereplicative phase of T4 development.
  Virol J, 7, 289.  
  21029432 E.P.Geiduschek, and G.A.Kassavetis (2010).
Transcription of the T4 late genes.
  Virol J, 7, 288.  
20615963 J.Chen, S.A.Darst, and D.Thirumalai (2010).
Promoter melting triggered by bacterial RNA polymerase occurs in three steps.
  Proc Natl Acad Sci U S A, 107, 12523-12528.  
20735776 J.Herrou, R.Foreman, A.Fiebig, and S.Crosson (2010).
A structural model of anti-anti-σ inhibition by a two-component receiver domain: the PhyR stress response regulator.
  Mol Microbiol, 78, 290-304.
PDB code: 3n0r
20088902 J.Schweer, H.Türkeri, B.Link, and G.Link (2010).
AtSIG6, a plastid sigma factor from Arabidopsis, reveals functional impact of cpCK2 phosphorylation.
  Plant J, 62, 192-202.  
19843224 K.Hollands, D.J.Lee, G.S.Lloyd, and S.J.Busby (2010).
Activation of sigma 28-dependent transcription in Escherichia coli by the cyclic AMP receptor protein requires an unusual promoter organization.
  Mol Microbiol, 75, 1098-1111.  
21149272 L.M.Bond, J.P.Peters, N.A.Becker, J.D.Kahn, and L.J.Maher (2010).
Gene repression by minimal lac loops in vivo.
  Nucleic Acids Res, 38, 8072-8082.  
20606072 M.K.Taha, S.T.Hedberg, M.Szatanik, E.Hong, C.Ruckly, R.Abad, S.Bertrand, F.Carion, H.Claus, A.Corso, R.Enríquez, S.Heuberger, W.Hryniewicz, K.A.Jolley, P.Kriz, M.Mollerach, M.Musilek, A.Neri, P.Olcén, M.Pana, A.Skoczynska, C.Sorhouet Pereira, P.Stefanelli, G.Tzanakaki, M.Unemo, J.A.Vázquez, U.Vogel, and I.Wasko (2010).
Multicenter study for defining the breakpoint for rifampin resistance in Neisseria meningitidis by rpoB sequencing.
  Antimicrob Agents Chemother, 54, 3651-3658.  
  20856905 N.Opalka, J.Brown, W.J.Lane, K.A.Twist, R.Landick, F.J.Asturias, and S.A.Darst (2010).
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.
  PLoS Biol, 8, 0.
PDB codes: 3lti 3lu0
20439713 P.C.Burrows, N.Joly, and M.Buck (2010).
A prehydrolysis state of an AAA+ ATPase supports transcription activation of an enhancer-dependent RNA polymerase.
  Proc Natl Acad Sci U S A, 107, 9376-9381.  
20070531 P.G.Devi, E.A.Campbell, S.A.Darst, and B.E.Nickels (2010).
Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation.
  Mol Microbiol, 75, 607-622.  
20483995 T.J.Gries, W.S.Kontur, M.W.Capp, R.M.Saecker, and M.T.Record (2010).
One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex.
  Proc Natl Acad Sci U S A, 107, 10418-10423.  
19895816 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
  J Mol Biol, 395, 686-704.  
19965383 X.Liu, D.A.Bushnell, D.Wang, G.Calero, and R.D.Kornberg (2010).
Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism.
  Science, 327, 206-209.
PDB code: 3k7a
20534498 Y.Yuzenkova, and N.Zenkin (2010).
Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis.
  Proc Natl Acad Sci U S A, 107, 10878-10883.  
20094031 Z.A.Chen, A.Jawhari, L.Fischer, C.Buchen, S.Tahir, T.Kamenski, M.Rasmussen, L.Lariviere, J.C.Bukowski-Wills, M.Nilges, P.Cramer, and J.Rappsilber (2010).
Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry.
  EMBO J, 29, 717-726.  
19538447 A.D.Klocko, and K.M.Wassarman (2009).
6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2.
  Mol Microbiol, 73, 152-164.  
19833764 A.Feklistov, and S.A.Darst (2009).
Promoter recognition by bacterial alternative sigma factors: the price of high selectivity?
  Genes Dev, 23, 2371-2375.  
19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
  Curr Opin Struct Biol, 19, 724-731.  
19578065 A.Rogozina, E.Zaychikov, M.Buckle, H.Heumann, and B.Sclavi (2009).
DNA melting by RNA polymerase at the T7A1 promoter precedes the rate-limiting step at 37 degrees C and results in the accumulation of an off-pathway intermediate.
  Nucleic Acids Res, 37, 5390-5404.  
19833768 B.M.Koo, V.A.Rhodius, G.Nonaka, P.L.deHaseth, and C.A.Gross (2009).
Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition.
  Genes Dev, 23, 2426-2436.  
  19903881 B.P.Hudson, J.Quispe, S.Lara-González, Y.Kim, H.M.Berman, E.Arnold, R.H.Ebright, and C.L.Lawson (2009).
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.
  Proc Natl Acad Sci U S A, 106, 19830-19835.
PDB code: 3iyd
19717606 C.L.Ross, K.S.Thomason, and T.M.Koehler (2009).
An extracytoplasmic function sigma factor controls beta-lactamase gene expression in Bacillus anthracis and other Bacillus cereus group species.
  J Bacteriol, 191, 6683-6693.  
19604473 C.Oubridge, D.A.Krummel, A.K.Leung, J.Li, and K.Nagai (2009).
Interpreting a low resolution map of human U1 snRNP using anomalous scatterers.
  Structure, 17, 930-938.  
19617357 C.W.Lennon, T.Gaal, W.Ross, and R.L.Gourse (2009).
Escherichia coli DksA binds to Free RNA polymerase with higher affinity than to RNA polymerase in an open complex.
  J Bacteriol, 191, 5854-5858.  
19109435 C.Y.Chen, C.C.Chang, C.F.Yen, M.T.Chiu, and W.H.Chang (2009).
Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis.
  Proc Natl Acad Sci U S A, 106, 127-132.  
19820686 D.Kostrewa, M.E.Zeller, K.J.Armache, M.Seizl, K.Leike, M.Thomm, and P.Cramer (2009).
RNA polymerase II-TFIIB structure and mechanism of transcription initiation.
  Nature, 462, 323-330.
PDB code: 3k1f
19735077 E.B.Johnston, P.J.Lewis, and R.Griffith (2009).
The interaction of Bacillus subtilis sigmaA with RNA polymerase.
  Protein Sci, 18, 2287-2297.  
18946472 G.A.Belogurov, M.N.Vassylyeva, A.Sevostyanova, J.R.Appleman, A.X.Xiang, R.Lira, S.E.Webber, S.Klyuyev, E.Nudler, I.Artsimovitch, and D.G.Vassylyev (2009).
Transcription inactivation through local refolding of the RNA polymerase structure.
  Nature, 457, 332-335.
PDB code: 3eql
19458260 H.Spåhr, G.Calero, D.A.Bushnell, and R.D.Kornberg (2009).
Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.
  Proc Natl Acad Sci U S A, 106, 9185-9190.
PDB code: 3h0g
19201973 I.Bakke, L.Berg, T.E.Aune, T.Brautaset, H.Sletta, A.Tøndervik, and S.Valla (2009).
Random mutagenesis of the PM promoter as a powerful strategy for improvement of recombinant-gene expression.
  Appl Environ Microbiol, 75, 2002-2011.  
19139410 I.G.Hook-Barnard, and D.M.Hinton (2009).
The promoter spacer influences transcription initiation via {sigma}70 region 1.1 of Escherichia coli RNA polymerase.
  Proc Natl Acad Sci U S A, 106, 737-742.  
18976666 L.A.Schroeder, T.J.Gries, R.M.Saecker, M.T.Record, M.E.Harris, and P.L.DeHaseth (2009).
Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA.
  J Mol Biol, 385, 339-349.  
19926275 M.X.Ho, B.P.Hudson, K.Das, E.Arnold, and R.H.Ebright (2009).
Structures of RNA polymerase-antibiotic complexes.
  Curr Opin Struct Biol, 19, 715-723.  
19111618 N.R.Gassman, S.O.Ho, Y.Korlann, J.Chiang, Y.Wu, L.J.Perry, Y.Kim, and S.Weiss (2009).
In vivo assembly and single-molecule characterization of the transcription machinery from Shewanella oneidensis MR-1.
  Protein Expr Purif, 65, 66-76.  
19441027 P.Yan, T.Wang, G.J.Newton, T.V.Knyushko, Y.Xiong, D.J.Bigelow, T.C.Squier, and M.U.Mayer (2009).
A targeted releasable affinity probe (TRAP) for in vivo photocrosslinking.
  Chembiochem, 10, 1507-1518.  
19150431 R.A.Mooney, S.E.Davis, J.M.Peters, J.L.Rowland, A.Z.Ansari, and R.Landick (2009).
Regulator trafficking on bacterial transcription units in vivo.
  Mol Cell, 33, 97.  
  19838335 S.Imamura, and M.Asayama (2009).
Sigma factors for cyanobacterial transcription.
  Gene Regul Syst Bio, 3, 65-87.  
19400800 S.J.Busby (2009).
More pieces in the promoter jigsaw: recognition of -10 regions by alternative sigma factors.
  Mol Microbiol, 72, 809-811.  
19171784 S.T.Rutherford, C.L.Villers, J.H.Lee, W.Ross, and R.L.Gourse (2009).
Allosteric control of Escherichia coli rRNA promoter complexes by DksA.
  Genes Dev, 23, 236-248.  
19805193 V.Nagy, K.C.Hsia, E.W.Debler, M.Kampmann, A.M.Davenport, G.Blobel, and A.Hoelz (2009).
Structure of a trimeric nucleoporin complex reveals alternate oligomerization states.
  Proc Natl Acad Sci U S A, 106, 17693-17698.
PDB code: 3iko
18952176 W.Ross, and R.L.Gourse (2009).
Analysis of RNA polymerase-promoter complex formation.
  Methods, 47, 13-24.  
18978051 Z.Hua, X.Rao, X.Feng, X.Luo, Y.Liang, and L.Shen (2009).
Mutagenesis of region 4 of sigma 28 from Chlamydia trachomatis defines determinants for protein-protein and protein-DNA interactions.
  J Bacteriol, 191, 651-660.  
18641146 A.Kanda, K.Tsuneishi, A.Mori, K.Ohnishi, A.Kiba, and Y.Hikichi (2008).
An amino acid substitution at position 740 in sigma70 of Ralstonia solanacearum strain OE1-1 affects its in planta growth.
  Appl Environ Microbiol, 74, 5841-5844.  
18296515 A.Kumar, and C.P.Moran (2008).
Promoter activation by repositioning of RNA polymerase.
  J Bacteriol, 190, 3110-3117.  
18208528 A.T.Cavanagh, A.D.Klocko, X.Liu, and K.M.Wassarman (2008).
Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70.
  Mol Microbiol, 67, 1242-1256.  
18363796 B.Swingle, D.Thete, M.Moll, C.R.Myers, D.J.Schneider, and S.Cartinhour (2008).
Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads.
  Mol Microbiol, 68, 871-889.  
18538653 C.D.Kaplan, K.M.Larsson, and R.D.Kornberg (2008).
The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin.
  Mol Cell, 30, 547-556.
PDB code: 3cqz
18272182 C.E.Vrentas, T.Gaal, M.B.Berkmen, S.T.Rutherford, S.P.Haugen, D.G.Vassylyev, W.Ross, and R.L.Gourse (2008).
Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation.
  J Mol Biol, 377, 551-564.  
18995832 D.Bose, T.Pape, P.C.Burrows, M.Rappas, S.R.Wigneshweraraj, M.Buck, and X.Zhang (2008).
Organization of an activator-bound RNA polymerase holoenzyme.
  Mol Cell, 32, 337-346.  
18375176 E.A.Campbell, L.F.Westblade, and S.A.Darst (2008).
Regulation of bacterial RNA polymerase sigma factor activity: a structural perspective.
  Curr Opin Microbiol, 11, 121-127.  
18940669 E.C.Schwartz, A.Shekhtman, K.Dutta, M.R.Pratt, D.Cowburn, S.Darst, and T.W.Muir (2008).
A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding.
  Chem Biol, 15, 1091-1103.
PDB code: 2k6x
18957204 J.Mukhopadhyay, K.Das, S.Ismail, D.Koppstein, M.Jang, B.Hudson, S.Sarafianos, S.Tuske, J.Patel, R.Jansen, H.Irschik, E.Arnold, and R.H.Ebright (2008).
The RNA polymerase "switch region" is a target for inhibitors.
  Cell, 135, 295-307.
PDB code: 3dxj
18155246 L.A.Schroeder, M.E.Karpen, and P.L.deHaseth (2008).
Threonine 429 of Escherichia coli sigma 70 is a key participant in promoter DNA melting by RNA polymerase.
  J Mol Biol, 376, 153-165.  
18281386 M.Djordjevic, and R.Bundschuh (2008).
Formation of the open complex by bacterial RNA polymerase--a quantitative model.
  Biophys J, 94, 4233-4248.  
18574242 N.Barinova, K.Kuznedelov, K.Severinov, and A.Kulbachinskiy (2008).
Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA.
  J Biol Chem, 283, 22482-22489.  
18219644 N.Minakawa, Y.Kawano, S.Murata, N.Inoue, and A.Matsuda (2008).
Oligodeoxynucleotides containing 3-bromo-3-deazaadenine and 7-bromo-7-deazaadenine 2'-deoxynucleosides as chemical probes to investigate DNA-protein interactions.
  Chembiochem, 9, 464-470.  
18818199 P.England, L.F.Westblade, G.Karimova, V.Robbe-Saule, F.Norel, and A.Kolb (2008).
Binding of the unorthodox transcription activator, Crl, to the components of the transcription machinery.
  J Biol Chem, 283, 33455-33464.  
18280161 S.Borukhov, and E.Nudler (2008).
RNA polymerase: the vehicle of transcription.
  Trends Microbiol, 16, 126-134.  
18287032 S.P.Haugen, W.Ross, M.Manrique, and R.L.Gourse (2008).
Fine structure of the promoter-sigma region 1.2 interaction.
  Proc Natl Acad Sci U S A, 105, 3292-3297.  
18521075 S.P.Haugen, W.Ross, and R.L.Gourse (2008).
Advances in bacterial promoter recognition and its control by factors that do not bind DNA.
  Nat Rev Microbiol, 6, 507-519.  
18331472 S.Wigneshweraraj, D.Bose, P.C.Burrows, N.Joly, J.Schumacher, M.Rappas, T.Pape, X.Zhang, P.Stockley, K.Severinov, and M.Buck (2008).
Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor.
  Mol Microbiol, 68, 538-546.  
18532976 Y.Onda, Y.Yagi, Y.Saito, N.Takenaka, and Y.Toyoshima (2008).
Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves: differential roles of cryptochrome 1 and cryptochrome 2 and dual function of SIG5 in the recognition of plastid promoters.
  Plant J, 55, 968-978.  
17763923 Y.Tutar (2008).
Chemical Linkage at Allosteric Activation of E. coli cAMP Receptor Protein.
  Protein J, 27, 21-29.  
18021805 Y.Yuzenkova, N.Zenkin, and K.Severinov (2008).
Mapping of RNA polymerase residues that interact with bacteriophage Xp10 transcription antitermination factor p7.
  J Mol Biol, 375, 29-35.  
17675424 A.Rieu, S.Weidmann, D.Garmyn, P.Piveteau, and J.Guzzo (2007).
Agr system of Listeria monocytogenes EGD-e: role in adherence and differential expression pattern.
  Appl Environ Microbiol, 73, 6125-6133.  
17302812 A.Typas, G.Becker, and R.Hengge (2007).
The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase.
  Mol Microbiol, 63, 1296-1306.  
17470797 C.A.Davis, C.A.Bingman, R.Landick, M.T.Record, and R.M.Saecker (2007).
Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase.
  Proc Natl Acad Sci U S A, 104, 7833-7838.  
18160040 K.C.Hsia, P.Stavropoulos, G.Blobel, and A.Hoelz (2007).
Architecture of a coat for the nuclear pore membrane.
  Cell, 131, 1313-1326.
PDB codes: 3bg0 3bg1
  17329813 K.Okada, H.Ichihara, H.Takahashi, N.Fujita, A.Ishihama, and T.Hakoshima (2007).
Preparation and preliminary X-ray diffraction analysis of crystals of bacterial flagellar sigma factor sigma 28 in complex with the sigma 28-binding region of its antisigma factor, FlgM.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 196-199.  
17567604 L.A.Schroeder, A.J.Choi, and P.L.DeHaseth (2007).
The -11A of promoter DNA and two conserved amino acids in the melting region of sigma70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact.
  Nucleic Acids Res, 35, 4141-4153.  
17997097 L.L.Beck, T.G.Smith, and T.R.Hoover (2007).
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17481658 M.Doucleff, J.G.Pelton, P.S.Lee, B.T.Nixon, and D.E.Wemmer (2007).
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PDB codes: 2o8k 2o9l
17409075 N.Osato, Y.Suzuki, K.Ikeo, and T.Gojobori (2007).
Transcriptional interferences in cis natural antisense transcripts of humans and mice.
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17268549 N.Zenkin, A.Kulbachinskiy, Y.Yuzenkova, A.Mustaev, I.Bass, K.Severinov, and K.Brodolin (2007).
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17670940 R.D.Kornberg (2007).
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17189297 R.K.Shultzaberger, Z.Chen, K.A.Lewis, and T.D.Schneider (2007).
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17253774 R.S.Turingan, C.Liu, M.E.Hawkins, and C.T.Martin (2007).
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17275836 T.J.Santangelo, L.Cubonová, C.L.James, and J.N.Reeve (2007).
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16798040 A.Feklistov, N.Barinova, A.Sevostyanova, E.Heyduk, I.Bass, I.Vvedenskaya, K.Kuznedelov, E.Merkiene, E.Stavrovskaya, S.Klimasauskas, V.Nikiforov, T.Heyduk, K.Severinov, and A.Kulbachinskiy (2006).
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17110578 A.N.Kapanidis, E.Margeat, S.O.Ho, E.Kortkhonjia, S.Weiss, and R.H.Ebright (2006).
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16420370 A.Typas, and R.Hengge (2006).
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17081994 B.E.Nickels, C.W.Roberts, J.W.Roberts, and A.Hochschild (2006).
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16819517 G.Miller, and S.Hahn (2006).
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The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.
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16341226 H.Kettenberger, A.Eisenführ, F.Brueckner, M.Theis, M.Famulok, and P.Cramer (2006).
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PDB code: 2b63
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16352826 J.E.Karlinsey, and K.T.Hughes (2006).
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16635801 J.J.Barker (2006).
Antibacterial drug discovery and structure-based design.
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16846227 L.M.Hsu, I.M.Cobb, J.R.Ozmore, M.Khoo, G.Nahm, L.Xia, Y.Bao, and C.Ahn (2006).
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16484205 M.J.Wilson, and I.L.Lamont (2006).
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16799558 P.Stavropoulos, G.Blobel, and A.Hoelz (2006).
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16601684 S.Nechaev, and E.P.Geiduschek (2006).
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16900098 T.A.Steitz (2006).
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16689632 T.Pan, and T.Sosnick (2006).
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16359326 Y.X.Huo, Z.X.Tian, M.Rappas, J.Wen, Y.C.Chen, C.H.You, X.Zhang, M.Buck, Y.P.Wang, and A.Kolb (2006).
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15687384 A.J.Smith, and N.J.Savery (2005).
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Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB.
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12700252 F.Narberhaus, and S.Balsiger (2003).
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Two distinct curved DNAs upstream of the light-responsive psbA gene in a cyanobacterium.
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An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4.
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12374751 G.A.Kassavetis, A.Grove, and E.P.Geiduschek (2002).
Effects of DNA strand breaks on transcription by RNA polymerase III: insights into the role of TFIIIB and the polarity of promoter opening.
  EMBO J, 21, 5508-5515.  
12220487 J.Frank (2002).
A cold look at transcription.
  Structure, 10, 1156-1157.  
12176389 J.L.Craighead, W.H.Chang, and F.J.Asturias (2002).
Structure of yeast RNA polymerase II in solution: implications for enzyme regulation and interaction with promoter DNA.
  Structure, 10, 1117-1125.  
12080337 L.M.Hsu (2002).
Open season on RNA polymerase.
  Nat Struct Biol, 9, 502-504.  
12377565 M.B.Schmid (2002).
Structural proteomics: the potential of high-throughput structure determination.
  Trends Microbiol, 10, S27-S31.  
12468233 P.Aloy, and R.B.Russell (2002).
The third dimension for protein interactions and complexes.
  Trends Biochem Sci, 27, 633-638.  
12457703 R.Hengge-Aronis (2002).
Stationary phase gene regulation: what makes an Escherichia coli promoter sigmaS-selective?
  Curr Opin Microbiol, 5, 591-595.  
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.