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PDBsum entry 1ddq

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protein metals Protein-protein interface(s) links
Transcription PDB id
1ddq
Jmol PyMol
Contents
Protein chains
226 a.a.
1112 a.a.
1077 a.a.
91 a.a.
Metals
_ZN
_MG
Superseded by: 1hqm 1hqm
PDB id:
1ddq
Name: Transcription
Title: Crystal structure of thermus aquaticus core RNA polymerase at 3.3 a resolution
Structure: DNA-directed RNA polymerase. Chain: a, b. Fragment: alpha subunit. DNA-directed RNA polymerase. Chain: c. Fragment: beta subunit. DNA-directed RNA polymerase. Chain: d. Fragment: beta-prime subunit.
Source: Thermus aquaticus. Bacteria. Bacteria
Resolution:
3.30Å     R-factor:   0.329     R-free:   0.399
Authors: G.Zhang,E.A.Campbell,L.Minakhin,C.Richter,K.Severinov, S.A.Darst
Key ref:
G.Zhang et al. (1999). Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell, 98, 811-824. PubMed id: 10499798 DOI: 10.1016/S0092-8674(00)81515-9
Date:
11-Nov-99     Release date:   28-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 226 a.a.
Protein chain
No UniProt id for this chain
Struc:  
Struc:  
Struc: 1112 a.a.
Protein chain
No UniProt id for this chain
Struc:  
Struc:  
Struc: 1077 a.a.
Protein chain
No UniProt id for this chain
Struc: 91 a.a.
Key:    Secondary structure  CATH domain

 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

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(00)81515-9 Cell 98:811-824 (1999)
PubMed id: 10499798  
 
 
Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution.
G.Zhang, E.A.Campbell, L.Minakhin, C.Richter, K.Severinov, S.A.Darst.
 
  ABSTRACT  
 
The X-ray crystal structure of Thermus aquaticus core RNA polymerase reveals a "crab claw"-shaped molecule with a 27 A wide internal channel. Located on the back wall of the channel is a Mg2+ ion required for catalytic activity, which is chelated by an absolutely conserved motif from all bacterial and eukaryotic cellular RNA polymerases. The structure places key functional sites, defined by mutational and cross-linking analysis, on the inner walls of the channel in close proximity to the active center Mg2+. Further out from the catalytic center, structural features are found that may be involved in maintaining the melted transcription bubble, clamping onto the RNA product and/or DNA template to assure processivity, and delivering nucleotide substrates to the active center.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The RNAP β and β′ SubunitsTwo stereo views of the RNAP structure (represented by transparent molecular surfaces), displayed using the program GRASP ([36]). The paths of the polypeptide backbone for β (top) or β′ (bottom) are shown as worms and color-coded with a gradient from the N to C terminus according to the scheme shown at the top of the figure (the color coding is also shown in Figure 1 with closer reference to the features of the primary structure). The nonconserved domain of β′ (residues 133–461) is not included in the color gradient. The surfaces are colored according to the worm color, or else are white for the other RNAP subunits. The Mg^2+ ion chelated at the active center is indicated by a magenta sphere. The Zn^2+ ion bound in β′ (see text) is indicated by a light green sphere.
Figure 7.
Figure 7. RNAP Structure–Function Relationship(a) Molecular surface representations of the “open book” views of the inside of the RNAP channel. The top row shows the inside, top surface of the channel (primarily β), and the bottom row shows the inside, bottom surface (primarily β′). Colored gray are the parts of the protein structure that have been sliced away. (The gray surfaces of the top and bottom views do not match because the slicing and viewing angles are different to afford the best views of the structural features discussed.) The active center Mg^2+ is visible as a magenta sphere. On the left, the sequence conservation is mapped onto the structure as in Figure 6. On the right, various functional sites determined from DNA and RNA cross-linking experiments are mapped onto the structure. The color coding is as follows: red, absolutely conserved -NADFDGD- motif of β′[D]; orange, cross-links to various probes positioned at the 3′-end of the RNA transcript ([29 and 40]); yellow, cross-links to various probes position at the 5′-end of the i site NTP substrate ( [33, 51 and 60]); green, cross-links from probes incorporated into specific positions of the template strand of the DNA ( [38]); blue, a cross-link mapped from a probe incorporated at the −10 position of the RNA transcript ( [40]).(b) Schematic model of the structure of a ternary transcription complex. Double-stranded DNA is represented as blue cylinders. The DNA template strand is shown as a blue line; the nontemplate strand, a cyan line; the RNA transcript, a red line. Very little information is available to position the nontemplate DNA strand within the model; it is shown here for illustrative purposes only. (Left) View with intact RNAP molecule. (Bottom) Same view but with parts of the RNAP cut away (shown in gray) to reveal the inner workings of the complex, which are labeled.
 
  The above figures are reprinted by permission from Cell Press: Cell (1999, 98, 811-824) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB code: 3qqc
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Evolution of multisubunit RNA polymerases in the three domains of life.
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X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
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PDB codes: 3q0a 3q22 3q23 3q24
21250781 S.H.Jun, M.J.Reichlen, M.Tajiri, and K.S.Murakami (2011).
Archaeal RNA polymerase and transcription regulation.
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21447716 S.R.Kennedy, and D.A.Erie (2011).
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20152155 A.A.Golosov, J.J.Warren, L.S.Beese, and M.Karplus (2010).
The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis.
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PDB codes: 3eyz 3ez5
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.
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20457751 D.Pupov, N.Miropolskaya, A.Sevostyanova, I.Bass, I.Artsimovitch, and A.Kulbachinskiy (2010).
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20360047 G.Ruprich-Robert, and P.Thuriaux (2010).
Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases.
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20615963 J.Chen, S.A.Darst, and D.Thirumalai (2010).
Promoter melting triggered by bacterial RNA polymerase occurs in three steps.
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20702425 L.F.Westblade, E.A.Campbell, C.Pukhrambam, J.C.Padovan, B.E.Nickels, V.Lamour, and S.A.Darst (2010).
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.
  Nucleic Acids Res, 38, 8357-8369.
PDB code: 3mlq
20080799 M.Numata, H.W.Chu, A.Dakhama, and D.R.Voelker (2010).
Pulmonary surfactant phosphatidylglycerol inhibits respiratory syncytial virus-induced inflammation and infection.
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Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.
  PLoS Biol, 8, 0.
PDB codes: 3lti 3lu0
20026480 R.Carter, and G.Drouin (2010).
The increase in the number of subunits in eukaryotic RNA polymerase III relative to RNA polymerase II is due to the permanent recruitment of general transcription factors.
  Mol Biol Evol, 27, 1035-1043.  
21034443 R.O.Weinzierl (2010).
The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain.
  BMC Biol, 8, 134.  
20833321 S.Payankaulam, L.M.Li, and D.N.Arnosti (2010).
Transcriptional repression: conserved and evolved features.
  Curr Biol, 20, R764-R771.  
21124318 S.Tagami, S.Sekine, T.Kumarevel, N.Hino, Y.Murayama, S.Kamegamori, M.Yamamoto, K.Sakamoto, and S.Yokoyama (2010).
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
  Nature, 468, 978-982.
PDB codes: 3aoh 3aoi
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.
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19895816 W.J.Lane, and S.A.Darst (2010).
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19895820 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: sequence analysis.
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20534498 Y.Yuzenkova, and N.Zenkin (2010).
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20497334 Z.Baharoglu, R.Lestini, S.Duigou, and B.Michel (2010).
RNA polymerase mutations that facilitate replication progression in the rep uvrD recF mutant lacking two accessory replicative helicases.
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19366670 A.H.Yuan, B.E.Nickels, and A.Hochschild (2009).
The bacteriophage T4 AsiA protein contacts the beta-flap domain of RNA polymerase.
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19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
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19243224 A.J.Gordon, J.A.Halliday, M.D.Blankschien, P.A.Burns, F.Yatagai, and C.Herman (2009).
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PDB code: 3h0g
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Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion.
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19486663 L.Mollazadeh-Beidokhti, F.Mohammad-Rafiee, and H.Schiessel (2009).
Active nucleosome displacement: a theoretical approach.
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19926275 M.X.Ho, B.P.Hudson, K.Das, E.Arnold, and R.H.Ebright (2009).
Structures of RNA polymerase-antibiotic complexes.
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19855007 N.Miropolskaya, I.Artsimovitch, S.Klimasauskas, V.Nikiforov, and A.Kulbachinskiy (2009).
Allosteric control of catalysis by the F loop of RNA polymerase.
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Sigma factors for cyanobacterial transcription.
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The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA.
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18787125 A.Feklistov, V.Mekler, Q.Jiang, L.F.Westblade, H.Irschik, R.Jansen, A.Mustaev, S.A.Darst, and R.H.Ebright (2008).
Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center.
  Proc Natl Acad Sci U S A, 105, 14820-14825.  
18235446 A.Hirata, B.J.Klein, and K.S.Murakami (2008).
The X-ray crystal structure of RNA polymerase from Archaea.
  Nature, 451, 851-854.
PDB codes: 2pa8 2pmz 3hkz
18296515 A.Kumar, and C.P.Moran (2008).
Promoter activation by repositioning of RNA polymerase.
  J Bacteriol, 190, 3110-3117.  
18264749 B.A.Knutson, and S.S.Broyles (2008).
Expansion of poxvirus RNA polymerase subunits sharing homology with corresponding subunits of RNA polymerase II.
  Virus Genes, 36, 307-311.  
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
18086878 F.Beckouet, S.Labarre-Mariotte, B.Albert, Y.Imazawa, M.Werner, O.Gadal, Y.Nogi, and P.Thuriaux (2008).
Two RNA polymerase I subunits control the binding and release of Rrn3 during transcription.
  Mol Cell Biol, 28, 1596-1605.  
18190515 F.Cava, M.A.de Pedro, E.Blas-Galindo, G.S.Waldo, L.F.Westblade, and J.Berenguer (2008).
Expression and use of superfolder green fluorescent protein at high temperatures in vivo: a tool to study extreme thermophile biology.
  Environ Microbiol, 10, 605-613.  
18468900 F.Werner (2008).
Structural evolution of multisubunit RNA polymerases.
  Trends Microbiol, 16, 247-250.  
18474389 J.A.Thomas, M.R.Rolando, C.A.Carroll, P.S.Shen, D.M.Belnap, S.T.Weintraub, P.Serwer, and S.C.Hardies (2008).
Characterization of Pseudomonas chlororaphis myovirus 201varphi2-1 via genomic sequencing, mass spectrometry, and electron microscopy.
  Virology, 376, 330-338.  
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
19055851 L.Tan, S.Wiesler, D.Trzaska, H.C.Carney, and R.O.Weinzierl (2008).
Bridge helix and trigger loop perturbations generate superactive RNA polymerases.
  J Biol, 7, 40.  
18573085 P.Cramer, K.J.Armache, S.Baumli, S.Benkert, F.Brueckner, C.Buchen, G.E.Damsma, S.Dengl, S.R.Geiger, A.J.Jasiak, A.Jawhari, S.Jennebach, T.Kamenski, H.Kettenberger, C.D.Kuhn, E.Lehmann, K.Leike, J.F.Sydow, and A.Vannini (2008).
Structure of eukaryotic RNA polymerases.
  Annu Rev Biophys, 37, 337-352.  
18280161 S.Borukhov, and E.Nudler (2008).
RNA polymerase: the vehicle of transcription.
  Trends Microbiol, 16, 126-134.  
18073196 S.Naji, M.G.Bertero, P.Spitalny, P.Cramer, and M.Thomm (2008).
Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement.
  Nucleic Acids Res, 36, 676-687.  
18025041 S.Nottebaum, L.Tan, D.Trzaska, H.C.Carney, and R.O.Weinzierl (2008).
The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes.
  Nucleic Acids Res, 36, 245-252.  
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.  
17763923 Y.Tutar (2008).
Chemical Linkage at Allosteric Activation of E. coli cAMP Receptor Protein.
  Protein J, 27, 21-29.  
17698847 A.Cheeran, N.R.Kolli, and R.Sen (2007).
The site of action of the antiterminator protein N from the lambdoid phage H-19B.
  J Biol Chem, 282, 30997-31007.  
17173017 A.Z.Ansari (2007).
Chemical crosshairs on the central dogma.
  Nat Chem Biol, 3, 2-7.  
17581590 D.G.Vassylyev, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, and I.Artsimovitch (2007).
Structural basis for transcription elongation by bacterial RNA polymerase.
  Nature, 448, 157-162.
PDB code: 2o5i
17581591 D.G.Vassylyev, M.N.Vassylyeva, J.Zhang, M.Palangat, I.Artsimovitch, and R.Landick (2007).
Structural basis for substrate loading in bacterial RNA polymerase.
  Nature, 448, 163-168.
PDB codes: 2o5j 2ppb
18064834 E.A.Kashkina, M.V.Anikin, W.T.McAllister, N.Kochetkov, and D.E.Temyakov (2007).
Determination of the melting site of the DNA duplex in the active center of bacterial RNA-polymerase by fluorescence quenching technique.
  Dokl Biochem Biophys, 416, 285-289.  
17766423 E.Stepanova, J.Lee, M.Ozerova, E.Semenova, K.Datsenko, B.L.Wanner, K.Severinov, and S.Borukhov (2007).
Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro.
  J Bacteriol, 189, 8772-8785.  
17679091 I.Toulokhonov, J.Zhang, M.Palangat, and R.Landick (2007).
A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing.
  Mol Cell, 27, 406-419.  
17160640 J.Luo, and B.D.Hall (2007).
A multistep process gave rise to RNA polymerase IV of land plants.
  J Mol Evol, 64, 101-112.  
18160031 J.R.Haag, and C.S.Pikaard (2007).
RNA polymerase I: a multifunctional molecular machine.
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  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.
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17711420 K.Severinov, E.Semenova, A.Kazakov, T.Kazakov, and M.S.Gelfand (2007).
Low-molecular-weight post-translationally modified microcins.
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17328674 M.Sharon, and C.V.Robinson (2007).
The role of mass spectrometry in structure elucidation of dynamic protein complexes.
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17670940 R.D.Kornberg (2007).
The molecular basis of eukaryotic transcription.
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17253774 R.S.Turingan, C.Liu, M.E.Hawkins, and C.T.Martin (2007).
Structural confirmation of a bent and open model for the initiation complex of T7 RNA polymerase.
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17960736 R.Weerasekera, Y.M.She, K.A.Markham, Y.Bai, N.Opalka, S.Orlicky, F.Sicheri, T.Kislinger, and G.Schmitt-Ulms (2007).
Interactome and interface protocol (2IP): a novel strategy for high sensitivity topology mapping of protein complexes.
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Upstream promoter sequences and alphaCTD mediate stable DNA wrapping within the RNA polymerase-promoter open complex.
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A system for heterologous expression and isolation of Escherichia coli RNA polymerase and its components.
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17875640 Y.Xiong, and Z.F.Burton (2007).
A tunable ratchet driving human RNA polymerase II translocation adjusted by accurately templated nucleoside triphosphates loaded at downstream sites and by elongation factors.
  J Biol Chem, 282, 36582-36592.  
16914440 E.Kashkina, M.Anikin, T.H.Tahirov, S.N.Kochetkov, D.G.Vassylyev, and D.Temiakov (2006).
Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations.
  Nucleic Acids Res, 34, 4036-4045.  
16635801 J.J.Barker (2006).
Antibacterial drug discovery and structure-based design.
  Drug Discov Today, 11, 391-404.  
16765888 J.Zlatanova, W.T.McAllister, S.Borukhov, and S.H.Leuba (2006).
Single-molecule approaches reveal the idiosyncrasies of RNA polymerases.
  Structure, 14, 953-966.  
17286098 K.D.Kuznedelov, N.V.Komissarova, and K.V.Severinov (2006).
The role of the bacterial RNA polymerase beta subunit flexible flap domain in transcription termination.
  Dokl Biochem Biophys, 410, 263-266.  
16597620 K.Potrykus, D.Vinella, H.Murphy, A.Szalewska-Palasz, R.D'Ari, and M.Cashel (2006).
Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA.
  J Biol Chem, 281, 15238-15248.  
17146456 P.Cramer (2006).
Deciphering the RNA polymerase II structure: a personal perspective.
  Nat Struct Mol Biol, 13, 1042-1044.  
16815708 P.Deighan, and A.Hochschild (2006).
Conformational toggle triggers a modulator of RNA polymerase activity.
  Trends Biochem Sci, 31, 424-426.  
17174884 R.Landick, and R.Kornberg (2006).
A long time in the making--the Nobel Prize for RNA polymerase.
  Cell, 127, 1087-1090.  
16908155 R.Mathew, and D.Chatterji (2006).
The evolving story of the omega subunit of bacterial RNA polymerase.
  Trends Microbiol, 14, 450-455.  
17098194 S.A.Kostek, P.Grob, S.De Carlo, J.S.Lipscomb, F.Garczarek, and E.Nogales (2006).
Molecular architecture and conformational flexibility of human RNA polymerase II.
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16621791 S.F.Holmes, T.J.Santangelo, C.K.Cunningham, J.W.Roberts, and D.A.Erie (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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16537373 V.R.Tadigotla, D.O Maoiléidigh, A.M.Sengupta, V.Epshtein, R.H.Ebright, E.Nudler, and A.E.Ruckenstein (2006).
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16475805 W.S.Kontur, R.M.Saecker, C.A.Davis, M.W.Capp, and M.T.Record (2006).
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15687384 A.J.Smith, and N.J.Savery (2005).
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15735307 A.M.Hansen, Y.Gu, M.Li, M.Andrykovitch, D.S.Waugh, D.J.Jin, and X.Ji (2005).
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15780938 A.Maitra, I.Shulgina, and V.J.Hernandez (2005).
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16169843 A.Niedziela-Majka, and T.Heyduk (2005).
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Structural basis for transcription inhibition by tagetitoxin.
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PDB code: 2be5
16039594 D.Jain, Y.Kim, K.L.Maxwell, S.Beasley, R.Zhang, G.N.Gussin, A.M.Edwards, and S.A.Darst (2005).
Crystal structure of bacteriophage lambda cII and its DNA complex.
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PDB codes: 1zpq 1zs4
15692574 E.A.Campbell, O.Pavlova, N.Zenkin, F.Leon, H.Irschik, R.Jansen, K.Severinov, and S.A.Darst (2005).
Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase.
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PDB codes: 1ynj 1ynn
15901712 E.Semenova, Y.Yuzenkova, J.Peduzzi, S.Rebuffat, and K.Severinov (2005).
Structure-activity analysis of microcinJ25: distinct parts of the threaded lasso molecule are responsible for interaction with bacterial RNA polymerase.
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15766545 F.Alber, M.F.Kim, and A.Sali (2005).
Structural characterization of assemblies from overall shape and subcomplex compositions.
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15680325 G.Bar-Nahum, V.Epshtein, A.E.Ruckenstein, R.Rafikov, A.Mustaev, and E.Nudler (2005).
A ratchet mechanism of transcription elongation and its control.
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15846841 H.L.Liu, and J.P.Hsu (2005).
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16141079 M.R.Stahley, and S.A.Strobel (2005).
Structural evidence for a two-metal-ion mechanism of group I intron splicing.
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15714199 S.J.Greive, and P.H.von Hippel (2005).
Thinking quantitatively about transcriptional regulation.
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Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.
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PDB codes: 1zyr 2cw0
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Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.
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PDB code: 1smy
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PDB codes: 1r9s 1r9t 1twa 1twc 1twf 1twg 1twh
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Topography of the euryarchaeal transcription initiation complex.
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Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase.
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High-efficiency generation of antibiotic-resistant strains of Streptococcus pneumoniae by PCR and transformation.
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From words to literature in structural proteomics.
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Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis.
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Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.
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RNA polymerase mutations that impair conversion to a termination-resistant complex by Q antiterminator proteins.
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Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase.
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NTP-driven translocation by human RNA polymerase II.
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Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution.
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The interaction between sigmaS, the stationary phase sigma factor, and the core enzyme of Escherichia coli RNA polymerase.
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Exploiting current understanding of antibiotic action for discovery of new drugs.
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E. coli Transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation.
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Using disulfide bond engineering to study conformational changes in the beta'260-309 coiled-coil region of Escherichia coli RNA polymerase during sigma(70) binding.
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12359719 L.C.Anthony, and R.R.Burgess (2002).
Conformational flexibility in sigma70 region 2 during transcription initiation.
  J Biol Chem, 277, 46433-46441.  
12080337 L.M.Hsu (2002).
Open season on RNA polymerase.
  Nat Struct Biol, 9, 502-504.  
11891334 L.Tsujikawa, O.V.Tsodikov, and P.L.deHaseth (2002).
Interaction of RNA polymerase with forked DNA: evidence for two kinetically significant intermediates on the pathway to the final complex.
  Proc Natl Acad Sci U S A, 99, 3493-3498.  
11856750 M.Kashlev, and N.Komissarova (2002).
Transcription termination: primary intermediates and secondary adducts.
  J Biol Chem, 277, 14501-14508.  
12198314 M.N.Vassylyeva, J.Lee, S.I.Sekine, O.Laptenko, S.Kuramitsu, T.Shibata, Y.Inoue, S.Borukhov, D.G.Vassylyev, and S.Yokoyama (2002).
Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus.
  Acta Crystallogr D Biol Crystallogr, 58, 1497-1500.  
11739720 M.Pal, and D.S.Luse (2002).
Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA.
  Mol Cell Biol, 22, 30-40.  
12453422 N.Komissarova, J.Becker, S.Solter, M.Kireeva, and M.Kashlev (2002).
Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination.
  Mol Cell, 10, 1151-1162.  
12193647 N.R.Forde, D.Izhaky, G.R.Woodcock, G.J.Wuite, and C.Bustamante (2002).
Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase.
  Proc Natl Acad Sci U S A, 99, 11682-11687.  
12210533 P.Cramer (2002).
Common structural features of nucleic acid polymerases.
  Bioessays, 24, 724-729.  
11839495 P.Cramer (2002).
Multisubunit RNA polymerases.
  Curr Opin Struct Biol, 12, 89-97.  
11904365 S.A.Darst, N.Opalka, P.Chacon, A.Polyakov, C.Richter, G.Zhang, and W.Wriggers (2002).
Conformational flexibility of bacterial RNA polymerase.
  Proc Natl Acad Sci U S A, 99, 4296-4301.  
11959501 S.K.Burley, and K.Kamada (2002).
Transcription factor complexes.
  Curr Opin Struct Biol, 12, 225-230.  
11809894 T.Bentin, and P.E.Nielsen (2002).
In vitro transcription of a torsionally constrained template.
  Nucleic Acids Res, 30, 803-809.  
12422209 T.H.Tahirov, D.Temiakov, M.Anikin, V.Patlan, W.T.McAllister, D.G.Vassylyev, and S.Yokoyama (2002).
Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution.
  Nature, 420, 43-50.
PDB code: 1h38
11779853 V.Van Mullem, M.Wery, M.Werner, J.Vandenhaute, and P.Thuriaux (2002).
The Rpb9 subunit of RNA polymerase II binds transcription factor TFIIE and interferes with the SAGA and elongator histone acetyltransferases.
  J Biol Chem, 277, 10220-10225.  
11167000 A.A.Best, and G.J.Olsen (2001).
Similar subunit architecture of archaeal and eukaryal RNA polymerases.
  FEMS Microbiol Lett, 195, 85-90.  
11397933 A.Klug (2001).
Structural biology. A marvellous machine for making messages.
  Science, 292, 1844-1846.  
11439189 B.A.Young, L.C.Anthony, T.M.Gruber, T.M.Arthur, E.Heyduk, C.Z.Lu, M.M.Sharp, T.Heyduk, R.R.Burgess, and C.A.Gross (2001).
A coiled-coil from the RNA polymerase beta' subunit allosterically induces selective nontemplate strand binding by sigma(70).
  Cell, 105, 935-944.  
11179888 C.W.Müller (2001).
Transcription factors: global and detailed views.
  Curr Opin Struct Biol, 11, 26-32.  
11290327 E.A.Campbell, N.Korzheva, A.Mustaev, K.Murakami, S.Nair, A.Goldfarb, and S.A.Darst (2001).
Structural mechanism for rifampicin inhibition of bacterial rna polymerase.
  Cell, 104, 901-912.
PDB code: 1i6v
11522828 E.A.Lesnik, R.Sampath, H.B.Levene, T.J.Henderson, J.A.McNeil, and D.J.Ecker (2001).
Prediction of rho-independent transcriptional terminators in Escherichia coli.
  Nucleic Acids Res, 29, 3583-3594.  
11489132 F.Colland, J.C.Rain, P.Gounon, A.Labigne, P.Legrain, and H.De Reuse (2001).
Identification of the Helicobacter pylori anti-sigma28 factor.
  Mol Microbiol, 41, 477-487.  
11168594 H.Sakurai, and A.Ishihama (2001).
Transcription organization and mRNA levels of the genes for all 12 subunits of the fission yeast RNA polymerase II.
  Genes Cells, 6, 25-36.  
11511351 J.E.Foster, S.F.Holmes, and D.A.Erie (2001).
Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation.
  Cell, 106, 243-252.  
11486042 J.F.Briand, F.Navarro, P.Rematier, C.Boschiero, S.Labarre, M.Werner, G.V.Shpakovski, and P.Thuriaux (2001).
Partners of Rpb8p, a small subunit shared by yeast RNA polymerases I, II and III.
  Mol Cell Biol, 21, 6056-6065.  
11309513 K.J.Harrington, R.B.Laughlin, and S.Liang (2001).
Balanced branching in transcription termination.
  Proc Natl Acad Sci U S A, 98, 5019-5024.  
11120893 K.Severinov (2001).
T7 RNA polymerase transcription complex: what you see is not what you get.
  Proc Natl Acad Sci U S A, 98, 5-7.  
11726518 L.G.Brieba, and R.Sousa (2001).
T7 promoter release mediated by DNA scrunching.
  EMBO J, 20, 6826-6835.  
11158566 L.Minakhin, S.Bhagat, A.Brunning, E.A.Campbell, S.A.Darst, R.H.Ebright, and K.Severinov (2001).
Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly.
  Proc Natl Acad Sci U S A, 98, 892-897.
PDB code: 1hqm
11114902 L.Minakhin, S.Nechaev, E.A.Campbell, and K.Severinov (2001).
Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription.
  J Bacteriol, 183, 71-76.  
11266593 N.Kannan, P.Chander, P.Ghosh, S.Vishveshwara, and D.Chatterji (2001).
Stabilizing interactions in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral and point mutation study.
  Protein Sci, 10, 46-54.  
11282465 N.Korzheva, and A.Mustaev (2001).
Transcription elongation complex: structure and function.
  Curr Opin Microbiol, 4, 119-125.  
11531998 P.Ghosh, A.Ishihama, and D.Chatterji (2001).
Escherichia coli RNA polymerase subunit omega and its N-terminal domain bind full-length beta' to facilitate incorporation into the alpha2beta subassembly.
  Eur J Biochem, 268, 4621-4627.  
11418764 R.Fedorov, V.Meshcheryakov, G.Gongadze, N.Fomenkova, N.Nevskaya, M.Selmer, M.Laurberg, O.Kristensen, S.Al-Karadaghi, A.Liljas, M.Garber, and S.Nikonov (2001).
Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins.
  Acta Crystallogr D Biol Crystallogr, 57, 968-976.
PDB code: 1feu
11282466 R.R.Burgess, and L.Anthony (2001).
How sigma docks to RNA polymerase and what sigma does.
  Curr Opin Microbiol, 4, 126-131.  
11389846 R.Sen, R.A.King, and R.A.Weisberg (2001).
Modification of the properties of elongating RNA polymerase by persistent association with nascent antiterminator RNA.
  Mol Cell, 7, 993.  
11738586 R.Sousa (2001).
A new level of regulation in transcription elongation?
  Trends Biochem Sci, 26, 695-697.  
11297923 S.A.Darst (2001).
Bacterial RNA polymerase.
  Curr Opin Struct Biol, 11, 155-162.  
  11747469 S.Grandemange, S.Schaller, S.Yamano, S.Du Manoir, G.V.Shpakovski, M.G.Mattei, C.Kedinger, and M.Vigneron (2001).
A human RNA polymerase II subunit is encoded by a recently generated multigene family.
  BMC Mol Biol, 2, 14.  
  11454743 S.Rozenfeld, and P.Thuriaux (2001).
A genetic look at the active site of RNA polymerase III.
  EMBO Rep, 2, 598-603.  
11987181 T.Heyduk, and A.Niedziela-Majka (2001).
Fluorescence resonance energy transfer analysis of escherichia coli RNA polymerase and polymerase-DNA complexes.
  Biopolymers, 61, 201-213.  
11511357 T.M.Gruber, D.Markov, M.M.Sharp, B.A.Young, C.Z.Lu, H.J.Zhong, I.Artsimovitch, K.M.Geszvain, T.M.Arthur, R.R.Burgess, R.Landick, K.Severinov, and C.A.Gross (2001).
Binding of the initiation factor sigma(70) to core RNA polymerase is a multistep process.
  Mol Cell, 8, 21-31.  
11433015 U.Fiedler, and H.T.Timmers (2001).
Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation.
  Nucleic Acids Res, 29, 2706-2714.  
11160910 V.Studitsky, K.Brodolin, Y.Liu, and A.Mirzabekov (2001).
Topography of lacUV5 initiation complexes.
  Nucleic Acids Res, 29, 854-861.  
11514661 W.A.Breyer, and B.W.Matthews (2001).
A structural basis for processivity.
  Protein Sci, 10, 1699-1711.  
11600705 W.Meng, T.Belyaeva, N.J.Savery, S.J.Busby, W.E.Ross, T.Gaal, R.L.Gourse, and M.S.Thomas (2001).
UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker.
  Nucleic Acids Res, 29, 4166-4178.  
11238372 W.Ross, A.Ernst, and R.L.Gourse (2001).
Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove.
  Genes Dev, 15, 491-506.  
11095728 A.Nedospasov, R.Rafikov, N.Beda, and E.Nudler (2000).
An autocatalytic mechanism of protein nitrosylation.
  Proc Natl Acad Sci U S A, 97, 13543-13548.  
10677518 B.Larsen, N.M.Wills, C.Nelson, J.F.Atkins, and R.F.Gesteland (2000).
Nonlinearity in genetic decoding: homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting.
  Proc Natl Acad Sci U S A, 97, 1683-1688.  
11063578 C.I.Wooddell, and R.R.Burgess (2000).
Topology of yeast RNA polymerase II subunits in transcription elongation complexes studied by photoaffinity cross-linking.
  Biochemistry, 39, 13405-13421.  
10779705 D.J.Studholme, and M.Buck (2000).
The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences.
  FEMS Microbiol Lett, 186, 1-9.  
  11004406 D.J.Studholme, and M.Buck (2000).
The alternative sigma factor sigma(28) of the extreme thermophile Aquifex aeolicus restores motility to an Escherichia coli fliA mutant.
  FEMS Microbiol Lett, 191, 103-107.  
10692367 D.J.Studholme, S.R.Wigneshwereraraj, M.T.Gallegos, and M.Buck (2000).
Functionality of purified sigma(N) (sigma(54)) and a NifA-like protein from the hyperthermophile Aquifex aeolicus.
  J Bacteriol, 182, 1616-1623.  
10777576 D.Kulish, J.Lee, I.Lomakin, B.Nowicka, A.Das, S.Darst, K.Normet, and S.Borukhov (2000).
The functional role of basic patch, a structural element of Escherichia coli transcript cleavage factors GreA and GreB.
  J Biol Chem, 275, 12789-12798.  
11046131 D.L.Pappas, and M.Hampsey (2000).
Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae.
  Mol Cell Biol, 20, 8343-8351.  
10766517 D.Rhodes, and S.K.Burley (2000).
Protein-nucleic acid interactions.
  Curr Opin Struct Biol, 10, 75-77.  
11095736 D.Temiakov, P.E.Mentesana, K.Ma, A.Mustaev, S.Borukhov, and W.T.McAllister (2000).
The specificity loop of T7 RNA polymerase interacts first with the promoter and then with the elongating transcript, suggesting a mechanism for promoter clearance.
  Proc Natl Acad Sci U S A, 97, 14109-14114.  
10841537 F.Todone, R.O.Weinzierl, P.Brick, and S.Onesti (2000).
Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target.
  Proc Natl Acad Sci U S A, 97, 6306-6310.
PDB code: 1dzf
10679468 G.M.Cheetham, and T.A.Steitz (2000).
Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases.
  Curr Opin Struct Biol, 10, 117-123.  
10860976 I.Artsimovitch, and R.Landick (2000).
Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals.
  Proc Natl Acad Sci U S A, 97, 7090-7095.  
11029421 I.Artsimovitch, V.Svetlov, L.Anthony, R.R.Burgess, and R.Landick (2000).
RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro.
  J Bacteriol, 182, 6027-6035.  
10788499 I.M.Donaldson, and J.D.Friesen (2000).
Zinc stoichiometry of yeast RNA polymerase II and characterization of mutations in the zinc-binding domain of the largest subunit.
  J Biol Chem, 275, 13780-13788.  
10744988 K.Severinov (2000).
RNA polymerase structure-function: insights into points of transcriptional regulation.
  Curr Opin Microbiol, 3, 118-125.  
11027286 M.Douziech, F.Coin, J.M.Chipoulet, Y.Arai, Y.Ohkuma, J.M.Egly, and B.Coulombe (2000).
Mechanism of promoter melting by the xeroderma pigmentosum complementation group B helicase of transcription factor IIH revealed by protein-DNA photo-cross-linking.
  Mol Cell Biol, 20, 8168-8177.  
10647296 M.Hampsey (2000).
RNA polymerase comes into focus.
  Trends Genet, 16, 20.  
11163202 M.T.Marr, and J.W.Roberts (2000).
Function of transcription cleavage factors GreA and GreB at a regulatory pause site.
  Mol Cell, 6, 1275-1285.  
10821700 N.Fujita, S.Endo, and A.Ishihama (2000).
Structural requirements for the interdomain linker of alpha subunit of Escherichia coli RNA polymerase.
  Biochemistry, 39, 6243-6249.  
10915625 N.Korzheva, A.Mustaev, M.Kozlov, A.Malhotra, V.Nikiforov, A.Goldfarb, and S.A.Darst (2000).
A structural model of transcription elongation.
  Science, 289, 619-625.  
10892647 N.Naryshkin, A.Revyakin, Y.Kim, V.Mekler, and R.H.Ebright (2000).
Structural organization of the RNA polymerase-promoter open complex.
  Cell, 101, 601-611.  
10639128 N.Opalka, R.A.Mooney, C.Richter, K.Severinov, R.Landick, and S.A.Darst (2000).
Direct localization of a beta-subunit domain on the three-dimensional structure of Escherichia coli RNA polymerase.
  Proc Natl Acad Sci U S A, 97, 617-622.  
10784442 P.Cramer, D.A.Bushnell, J.Fu, A.L.Gnatt, B.Maier-Davis, N.E.Thompson, R.R.Burgess, A.M.Edwards, P.R.David, and R.D.Kornberg (2000).
Architecture of RNA polymerase II and implications for the transcription mechanism.
  Science, 288, 640-649.
PDB code: 1en0
10958696 P.F.Cliften, S.H.Jang, and J.A.Jaehning (2000).
Identifying a core RNA polymerase surface critical for interactions with a sigma-like specificity factor.
  Mol Cell Biol, 20, 7013-7023.  
  10673505 Q.Tan, K.L.Linask, R.H.Ebright, and N.A.Woychik (2000).
Activation mutants in yeast RNA polymerase II subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria.
  Genes Dev, 14, 339-348.  
11118218 R.D.Finn, E.V.Orlova, B.Gowen, M.Buck, and M.van Heel (2000).
Escherichia coli RNA polymerase core and holoenzyme structures.
  EMBO J, 19, 6833-6844.  
10972792 R.L.Gourse, W.Ross, and T.Gaal (2000).
UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition.
  Mol Microbiol, 37, 687-695.  
10973050 S.A.Datwyler, and C.F.Meares (2000).
Protein-protein interactions mapped by artificial proteases: where sigma factors bind to RNA polymerase.
  Trends Biochem Sci, 25, 408-414.  
10801469 S.Buratowski (2000).
Snapshots of RNA polymerase II transcription initiation.
  Curr Opin Cell Biol, 12, 320-325.  
10856247 S.R.Wigneshweraraj, N.Fujita, A.Ishihama, and M.Buck (2000).
Conservation of sigma-core RNA polymerase proximity relationships between the enhancer-independent and enhancer-dependent sigma classes.
  EMBO J, 19, 3038-3048.  
10723029 U.Fiedler, and H.T.Marc Timmers (2000).
Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.
  Bioessays, 22, 316-326.  
10970887 Y.Guo, C.M.Lew, and J.D.Gralla (2000).
Promoter opening by sigma(54) and sigma(70) RNA polymerases: sigma factor-directed alterations in the mechanism and tightness of control.
  Genes Dev, 14, 2242-2255.  
10499791 R.A.Mooney, and R.Landick (1999).
RNA polymerase unveiled.
  Cell, 98, 687-690.  
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.

 

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