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PDBsum entry 2o5i

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protein dna_rna metals Protein-protein interface(s) links
Transferase/DNA-RNA hybrid PDB id
2o5i
Jmol
Contents
Protein chains
229 a.a. *
1119 a.a. *
1303 a.a. *
95 a.a. *
DNA/RNA
Metals
_MG ×2
_ZN ×4
Waters ×3563
* Residue conservation analysis
PDB id:
2o5i
Name: Transferase/DNA-RNA hybrid
Title: Crystal structure of the t. Thermophilus RNA polymerase elon complex
Structure: 5'-d(p Cp Cp Cp Tp Gp Tp Cp Tp Gp Gp Cp Gp Tp Tp P Cp Gp Cp Cp G)-3'. Chain: g, x. Engineered: yes. Other_details: DNA template strand. 5'-r(p Gp Ap Gp Up Cp Up Gp Cp Gp Gp Cp Gp Cp Gp Chain: h, y. Engineered: yes. Other_details: RNA transcript.
Source: Synthetic: yes. Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Strain: hb8
Resolution:
2.50Å     R-factor:   0.238     R-free:   0.267
Authors: D.G.Vassylyev,T.H.Tahirov,M.N.Vassylyeva
Key ref:
D.G.Vassylyev et al. (2007). Structural basis for transcription elongation by bacterial RNA polymerase. Nature, 448, 157-162. PubMed id: 17581590 DOI: 10.1038/nature05932
Date:
06-Dec-06     Release date:   03-Jul-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5SHR6  (RPOA_THET8) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
315 a.a.
229 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE9  (RPOB_THET8) -  DNA-directed RNA polymerase subunit beta
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1119 a.a.
1119 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE8  (RPOC_THET8) -  DNA-directed RNA polymerase subunit beta'
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1524 a.a.
1303 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega
Seq:
Struc:
99 a.a.
95 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, K, L, M, N, O: 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!
  Biological process     DNA repair   2 terms 
  Biochemical function     transferase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nature05932 Nature 448:157-162 (2007)
PubMed id: 17581590  
 
 
Structural basis for transcription elongation by bacterial RNA polymerase.
D.G.Vassylyev, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, I.Artsimovitch.
 
  ABSTRACT  
 
The RNA polymerase elongation complex (EC) is both highly stable and processive, rapidly extending RNA chains for thousands of nucleotides. Understanding the mechanisms of elongation and its regulation requires detailed information about the structural organization of the EC. Here we report the 2.5-A resolution structure of the Thermus thermophilus EC; the structure reveals the post-translocated intermediate with the DNA template in the active site available for pairing with the substrate. DNA strand separation occurs one position downstream of the active site, implying that only one substrate at a time can specifically bind to the EC. The upstream edge of the RNA/DNA hybrid stacks on the beta'-subunit 'lid' loop, whereas the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination.
 
  Selected figure(s)  
 
Figure 3.
Figure 3: Schematic drawing of the protein/nucleic acid contacts. Polar and stacking interactions are shown as black and green arrows, respectively. The (i + 1) non-template nucleotide was not resolved in the electron density map and is therefore not shown.
Figure 5.
Figure 5: dwDNA and RNA/DNA hybrid strand separation. a, b, Structural elements interacting with the +2 dwDNA base pair in the ttEC (a) and T7 EC (b). c, The lid loop stacks on the upstream RNA/DNA base pair in the ttEC. d, The first displaced RNA base is trapped in the protein pocket formed by the displacement loop in the ttEC. The van der Waals and polar interactions are shown by cyan and blue dashed lines, respectively.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 448, 157-162) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21187417 B.J.Klein, D.Bose, K.J.Baker, Z.M.Yusoff, X.Zhang, and K.S.Murakami (2011).
RNA polymerase and transcription elongation factor Spt4/5 complex structure.
  Proc Natl Acad Sci U S A, 108, 546-550.
PDB code: 3p8b
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.  
  21435034 G.Swapna, A.Chakraborty, V.Kumari, R.Sen, and V.Nagaraja (2011).
Mutations in β' subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance.
  Mol Microbiol, 80, 1169-1185.  
21265743 H.Heindl, P.Greenwell, N.Weingarten, T.Kiss, G.Terstyanszky, and R.O.Weinzierl (2011).
Cation-π interactions induce kinking of a molecular hinge in the RNA polymerase bridge-helix domain.
  Biochem Soc Trans, 39, 31-35.  
21292158 M.H.Larson, R.Landick, and S.M.Block (2011).
Single-molecule studies of RNA polymerase: one singular sensation, every little step it takes.
  Mol Cell, 41, 249-262.  
21447716 S.R.Kennedy, and D.A.Erie (2011).
Templated nucleoside triphosphate binding to a noncatalytic site on RNA polymerase regulates transcription.
  Proc Natl Acad Sci U S A, 108, 6079-6084.  
21255416 V.A.Lyubetsky, O.A.Zverkov, L.I.Rubanov, and A.V.Seliverstov (2011).
Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level.
  Biol Direct, 6, 3.  
20639538 A.Sevostyanova, and I.Artsimovitch (2010).
Functional analysis of Thermus thermophilus transcription factor NusG.
  Nucleic Acids Res, 38, 7432-7445.  
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.  
  20384694 A.V.Yakhnin, and P.Babitzke (2010).
Mechanism of NusG-stimulated pausing, hairpin-dependent pause site selection and intrinsic termination at overlapping pause and termination sites in the Bacillus subtilis trp leader.
  Mol Microbiol, 76, 690-705.  
  21029433 D.M.Hinton (2010).
Transcriptional control in the prereplicative phase of T4 development.
  Virol J, 7, 289.  
20457751 D.Pupov, N.Miropolskaya, A.Sevostyanova, I.Bass, I.Artsimovitch, and A.Kulbachinskiy (2010).
Multiple roles of the RNA polymerase {beta}' SW2 region in transcription initiation, promoter escape, and RNA elongation.
  Nucleic Acids Res, 38, 5784-5796.  
20132437 G.A.Belogurov, A.Sevostyanova, V.Svetlov, and I.Artsimovitch (2010).
Functional regions of the N-terminal domain of the antiterminator RfaH.
  Mol Microbiol, 76, 286-301.  
20360047 G.Ruprich-Robert, and P.Thuriaux (2010).
Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases.
  Nucleic Acids Res, 38, 4559-4569.  
19966797 J.Zhang, M.Palangat, and R.Landick (2010).
Role of the RNA polymerase trigger loop in catalysis and pausing.
  Nat Struct Mol Biol, 17, 99.  
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
  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
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.  
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.  
20696893 S.E.Cohen, C.A.Lewis, R.A.Mooney, M.A.Kohanski, J.J.Collins, R.Landick, and G.C.Walker (2010).
Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli.
  Proc Natl Acad Sci U S A, 107, 15517-15522.  
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
20535204 T.H.Tahirov, N.D.Babayeva, K.Varzavand, J.J.Cooper, S.C.Sedore, and D.H.Price (2010).
Crystal structure of HIV-1 Tat complexed with human P-TEFb.
  Nature, 465, 747-751.
PDB codes: 3mi9 3mia
20079749 V.B.Agarkar, N.D.Babayeva, P.J.Wilder, A.Rizzino, and T.H.Tahirov (2010).
Crystal structure of mouse Elf3 C-terminal DNA-binding domain in complex with type II TGF-beta receptor promoter DNA.
  J Mol Biol, 397, 278-289.
PDB code: 3jtg
20075920 V.Epshtein, D.Dutta, J.Wade, and E.Nudler (2010).
An allosteric mechanism of Rho-dependent transcription termination.
  Nature, 463, 245-249.  
19895816 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
  J Mol Biol, 395, 686-704.  
19895820 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: sequence analysis.
  J Mol Biol, 395, 671-685.  
20798057 X.Huang, D.Wang, D.R.Weiss, D.A.Bushnell, R.D.Kornberg, and M.Levitt (2010).
RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription.
  Proc Natl Acad Sci U S A, 107, 15745-15750.  
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.
  Mol Microbiol, 77, 324-336.  
19605532 A.C.Rhee, B.H.Somerlot, N.Parimi, and J.M.Gott (2009).
Distinct roles for sequences upstream of and downstream from Physarum editing sites.
  RNA, 15, 1753-1765.  
19366670 A.H.Yuan, B.E.Nickels, and A.Hochschild (2009).
The bacteriophage T4 AsiA protein contacts the beta-flap domain of RNA polymerase.
  Proc Natl Acad Sci U S A, 106, 6597-6602.  
19941825 C.P.Guy, J.Atkinson, M.K.Gupta, A.A.Mahdi, E.J.Gwynn, C.J.Rudolph, P.B.Moon, I.C.van Knippenberg, C.J.Cadman, M.S.Dillingham, R.G.Lloyd, and P.McGlynn (2009).
Rep provides a second motor at the replisome to promote duplication of protein-bound DNA.
  Mol Cell, 36, 654-666.  
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.  
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.  
19489723 E.Nudler (2009).
RNA polymerase active center: the molecular engine of transcription.
  Annu Rev Biochem, 78, 335-361.  
19481445 F.Brueckner, J.Ortiz, and P.Cramer (2009).
A movie of the RNA polymerase nucleotide addition cycle.
  Curr Opin Struct Biol, 19, 294-299.  
19171965 F.Brueckner, K.J.Armache, A.Cheung, G.E.Damsma, H.Kettenberger, E.Lehmann, J.Sydow, and P.Cramer (2009).
Structure-function studies of the RNA polymerase II elongation complex.
  Acta Crystallogr D Biol Crystallogr, 65, 112-120.  
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
19560423 J.F.Sydow, F.Brueckner, A.C.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, and P.Cramer (2009).
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
  Mol Cell, 34, 710-721.
PDB codes: 3hou 3hov 3how 3hox 3hoy 3hoz
19416863 M.L.Kireeva, and M.Kashlev (2009).
Mechanism of sequence-specific pausing of bacterial RNA polymerase.
  Proc Natl Acad Sci U S A, 106, 8900-8905.  
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.  
19855007 N.Miropolskaya, I.Artsimovitch, S.Klimasauskas, V.Nikiforov, and A.Kulbachinskiy (2009).
Allosteric control of catalysis by the F loop of RNA polymerase.
  Proc Natl Acad Sci U S A, 106, 18942-18947.  
19535338 S.Dengl, and P.Cramer (2009).
Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro.
  J Biol Chem, 284, 21270-21279.
PDB code: 3h3v
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.  
19321439 T.Kent, E.Kashkina, M.Anikin, and D.Temiakov (2009).
Maintenance of RNA-DNA Hybrid Length in Bacterial RNA Polymerases.
  J Biol Chem, 284, 13497-13504.  
19651989 X.Rao, P.Deighan, Z.Hua, X.Hu, J.Wang, M.Luo, J.Wang, Y.Liang, G.Zhong, A.Hochschild, and L.Shen (2009).
A regulator from Chlamydia trachomatis modulates the activity of RNA polymerase through direct interaction with the beta subunit and the primary sigma subunit.
  Genes Dev, 23, 1818-1829.  
19680289 X.Yang, S.Molimau, G.P.Doherty, E.B.Johnston, J.Marles-Wright, R.Rothnagel, B.Hankamer, R.J.Lewis, and P.J.Lewis (2009).
The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA.
  EMBO Rep, 10, 997.  
19383448 Y.R.Yamada, and C.S.Peskin (2009).
A look-ahead model for the elongation dynamics of transcription.
  Biophys J, 96, 3015-3031.  
18022639 A.Dimitri, A.K.Goodenough, F.P.Guengerich, S.Broyde, and D.A.Scicchitano (2008).
Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
  J Mol Biol, 375, 353-366.  
  18818516 A.G.Baranovskiy, N.D.Babayeva, V.G.Liston, I.B.Rogozin, E.V.Koonin, Y.I.Pavlov, D.G.Vassylyev, and T.H.Tahirov (2008).
X-ray structure of the complex of regulatory subunits of human DNA polymerase delta.
  Cell Cycle, 7, 3026-3036.
PDB code: 3e0j
18849988 A.Muschielok, J.Andrecka, A.Jawhari, F.Brückner, P.Cramer, and J.Michaelis (2008).
A nano-positioning system for macromolecular structural analysis.
  Nat Methods, 5, 965-971.  
18195372 A.Sevostyanova, V.Svetlov, D.G.Vassylyev, and I.Artsimovitch (2008).
The elongation factor RfaH and the initiation factor {sigma} bind to the same site on the transcription elongation complex.
  Proc Natl Acad Sci U S A, 105, 865-870.  
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
19090964 C.D.Kaplan, and R.D.Kornberg (2008).
A bridge to transcription by RNA polymerase.
  J Biol, 7, 39.  
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.  
18482981 D.Dutta, J.Chalissery, and R.Sen (2008).
Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNA.
  J Biol Chem, 283, 20243-20251.  
18552824 F.Brueckner, and P.Cramer (2008).
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.
  Nat Struct Mol Biol, 15, 811-818.
PDB code: 2vum
18468900 F.Werner (2008).
Structural evolution of multisubunit RNA polymerases.
  Trends Microbiol, 16, 247-250.  
18162559 J.Andrecka, R.Lewis, F.Brückner, E.Lehmann, P.Cramer, and J.Michaelis (2008).
Single-molecule tracking of mRNA exiting from RNA polymerase II.
  Proc Natl Acad Sci U S A, 105, 135-140.  
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
18657503 J.N.Kuehner, and D.A.Brow (2008).
Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation.
  Mol Cell, 31, 201-211.  
18729732 J.W.Roberts, S.Shankar, and J.J.Filter (2008).
RNA polymerase elongation factors.
  Annu Rev Microbiol, 62, 211-233.  
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.  
19000817 M.Guo, F.Xu, J.Yamada, T.Egelhofer, Y.Gao, G.A.Hartzog, M.Teng, and L.Niu (2008).
Core structure of the yeast spt4-spt5 complex: a conserved module for regulation of transcription elongation.
  Structure, 16, 1649-1658.  
18358810 M.H.Larson, W.J.Greenleaf, R.Landick, and S.M.Block (2008).
Applied force reveals mechanistic and energetic details of transcription termination.
  Cell, 132, 971-982.  
18716630 M.Kwapisz, M.Wery, D.Després, Y.Ghavi-Helm, J.Soutourina, P.Thuriaux, and F.Lacroute (2008).
Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways.
  EMBO J, 27, 2411-2421.  
18538654 M.L.Kireeva, Y.A.Nedialkov, G.H.Cremona, Y.A.Purtov, L.Lubkowska, F.Malagon, Z.F.Burton, J.N.Strathern, and M.Kashlev (2008).
Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation.
  Mol Cell, 30, 557-566.  
18775328 N.Komissarova, T.Velikodvorskaya, R.Sen, R.A.King, S.Banik-Maiti, and R.A.Weisberg (2008).
Inhibition of a transcriptional pause by RNA anchoring to RNA polymerase.
  Mol Cell, 31, 683-694.  
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.  
18832144 P.Deighan, C.M.Diez, M.Leibman, A.Hochschild, and B.E.Nickels (2008).
The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase.
  Proc Natl Acad Sci U S A, 105, 15305-15310.  
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.  
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.  
18647607 Y.X.Mejia, H.Mao, N.R.Forde, and C.Bustamante (2008).
Thermal probing of E. coli RNA polymerase off-pathway mechanisms.
  J Mol Biol, 382, 628-637.  
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.  
17724015 A.Schwartz, E.Margeat, A.R.Rahmouni, and M.Boudvillain (2007).
Transcription termination factor rho can displace streptavidin from biotinylated RNA.
  J Biol Chem, 282, 31469-31476.  
17697097 F.Werner (2007).
Structure and function of archaeal RNA polymerases.
  Mol Microbiol, 65, 1395-1404.  
18059450 I.Artsimovitch, and D.G.Vassylyev (2007).
Merging the RNA and DNA worlds.
  Nat Struct Mol Biol, 14, 1122-1123.  
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.  
17725561 K.Sipos, R.Szigeti, X.Dong, and C.L.Turnbough (2007).
Systematic mutagenesis of the thymidine tract of the pyrBI attenuator and its effects on intrinsic transcription termination in Escherichia coli.
  Mol Microbiol, 66, 127-138.  
17625551 P.Cramer (2007).
Gene transcription: extending the message.
  Nature, 448, 142-143.  
18158897 V.Epshtein, C.J.Cardinale, A.E.Ruckenstein, S.Borukhov, and E.Nudler (2007).
An allosteric path to transcription termination.
  Mol Cell, 28, 991.  
17711918 V.Svetlov, G.A.Belogurov, E.Shabrova, D.G.Vassylyev, and I.Artsimovitch (2007).
Allosteric control of the RNA polymerase by the elongation factor RfaH.
  Nucleic Acids Res, 35, 5694-5705.  
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.  
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.