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PDBsum entry 1r9t

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protein dna_rna ligands metals Protein-protein interface(s) links
Transcription/DNA-RNA hybrid PDB id
1r9t
Jmol
Contents
Protein chains
1395 a.a. *
1106 a.a. *
266 a.a. *
214 a.a. *
84 a.a. *
133 a.a. *
119 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
DNA/RNA
Ligands
ATP
Metals
_ZN ×8
_MG ×2
* Residue conservation analysis
PDB id:
1r9t
Name: Transcription/DNA-RNA hybrid
Title: RNA polymerase ii strand separated elongation complex, mismatched nucleotide
Structure: RNA strand. Chain: r. Engineered: yes. Other_details: transcript. DNA template strand. Chain: t. Engineered: yes. DNA nontemplate strand. Chain: n.
Source: Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: delta-rpb4. Strain: delta-rpb4
Biol. unit: 13mer (from PQS)
Resolution:
3.50Å     R-factor:   0.230     R-free:   0.317
Authors: K.D.Westover,D.A.Bushnell,R.D.Kornberg
Key ref:
K.D.Westover et al. (2004). Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell, 119, 481-489. PubMed id: 15537538 DOI: 10.1016/j.cell.2004.10.016
Date:
30-Oct-03     Release date:   16-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1733 a.a.
1395 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1224 a.a.
1106 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3
Seq:
Struc:
318 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
Seq:
Struc:
215 a.a.
214 a.a.
Protein chain
Pfam   ArchSchema ?
P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2
Seq:
Struc:
155 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
Seq:
Struc:
146 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9
Seq:
Struc:
122 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5
Seq:
Struc:
70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11
Seq:
Struc:
120 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4
Seq:
Struc:
70 a.a.
46 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: 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
Bound ligand (Het Group name = ATP)
matches with 65.00% similarity
+ 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   7 terms 
  Biological process     transcription, RNA-dependent   14 terms 
  Biochemical function     RNA polymerase II activity     14 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.cell.2004.10.016 Cell 119:481-489 (2004)
PubMed id: 15537538  
 
 
Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
K.D.Westover, D.A.Bushnell, R.D.Kornberg.
 
  ABSTRACT  
 
Binding of a ribonucleoside triphosphate to an RNA polymerase II transcribing complex, with base pairing to the template DNA, was revealed by X-ray crystallography. Binding of a mismatched nucleoside triphosphate was also detected, but in an adjacent site, inverted with respect to the correctly paired nucleotide. The results are consistent with a two-step mechanism of nucleotide selection, with initial binding to an entry (E) site beneath the active center in an inverted orientation, followed by rotation into the nucleotide addition (A) site for pairing with the template DNA. This mechanism is unrelated to that of single subunit RNA polymerases and so defines a new paradigm for the large, multisubunit enzymes. Additional findings from these studies include a third nucleotide binding site that may define the length of backtracked RNA; DNA double helix unwinding in advance of the polymerase active center; and extension of the diffraction limit of RNA polymerase II crystals to 2.3 A.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Downstream End of the DNA-RNA Hybrid in Transcribing Complex Structures, Showing Occupancy of the A and E Sites(A) Transcribing complex with matched NTP (UTP) in the A site.(B) Transcribing complex with mismatched NTP (ATP) in the E site. Views are the same as in Figure 1. DNA is blue, RNA is red, and NTPs are in yellow. Mg ions are shown as magenta spheres.
Figure 5.
Figure 5. Substrate Entry to Active Center Regions of Single and Multisubunit PolymerasesSolvent-accessible surfaces for transcribing complexes of (A) pol II and (B) T7 RNA polymerase (PDB 1H38) are shown, in a “front” view of pol II (Cramer et al., 2000) and corresponding view of the T7 enzyme (aligned on the sugar-phosphate backbone of the DNA-RNA hybrid) (Tahirov et al., 2002), with the front portion of the proteins cut away to reveal the DNA-RNA hybrid (DNA blue, RNA red). A mismatched NTP bound to pol II as in Figure 2D is shown in pink. The direction of substrate entry to the active center is indicated by a black arrow.
 
  The above figures are reprinted by permission from Cell Press: Cell (2004, 119, 481-489) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21382609 I.Capek (2011).
Dispersions based on noble metal nanoparticles-DNA conjugates.
  Adv Colloid Interface Sci, 163, 123-143.  
21265742 M.Wojtas, B.Peralta, M.Ondiviela, M.Mogni, S.D.Bell, and N.G.Abrescia (2011).
Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.
  Biochem Soc Trans, 39, 25-30.
PDB code: 2y0s
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.  
19567268 C.Domecq, M.Kireeva, J.Archambault, M.Kashlev, B.Coulombe, and Z.F.Burton (2010).
Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II.
  Protein Expr Purif, 69, 83-90.  
20448203 D.Wang, G.Zhu, X.Huang, and S.J.Lippard (2010).
X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct.
  Proc Natl Acad Sci U S A, 107, 9584-9589.
PDB codes: 3m3y 3m4o
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.  
20088966 H.Koyama, T.Ueda, T.Ito, and K.Sekimizu (2010).
Novel RNA polymerase II mutation suppresses transcriptional fidelity and oxidative stress sensitivity in rpb9Delta yeast.
  Genes Cells, 15, 151-159.  
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
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.  
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
19439405 C.Walmacq, M.L.Kireeva, J.Irvin, Y.Nedialkov, L.Lubkowska, F.Malagon, J.N.Strathern, and M.Kashlev (2009).
Rpb9 Subunit Controls Transcription Fidelity by Delaying NTP Sequestration in RNA Polymerase II.
  J Biol Chem, 284, 19601-19612.  
19896365 D.G.Vassylyev (2009).
Elongation by RNA polymerase: a race through roadblocks.
  Curr Opin Struct Biol, 19, 691-700.  
19478184 D.Wang, D.A.Bushnell, X.Huang, K.D.Westover, M.Levitt, and R.D.Kornberg (2009).
Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
  Science, 324, 1203-1206.
PDB codes: 3gtg 3gtj 3gtk 3gto 3gtp 3gtq
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.  
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
19620213 J.Andrecka, B.Treutlein, M.A.Arcusa, A.Muschielok, R.Lewis, A.C.Cheung, P.Cramer, and J.Michaelis (2009).
Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex.
  Nucleic Acids Res, 37, 5803-5809.  
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.  
19289466 P.A.Meyer, P.Ye, M.H.Suh, M.Zhang, and J.Fu (2009).
Structure of the 12-Subunit RNA Polymerase II Refined with the Aid of Anomalous Diffraction Data.
  J Biol Chem, 284, 12933-12939.
PDB code: 3fki
19419240 Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, and N.G.Abrescia (2009).
Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
  PLoS Biol, 7, e102.
PDB codes: 2waq 2wb1
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
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.  
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.  
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
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.  
18084032 J.Gerber, A.Reiter, R.Steinbauer, S.Jakob, C.D.Kuhn, P.Cramer, J.Griesenbeck, P.Milkereit, and H.Tschochner (2008).
Site specific phosphorylation of yeast RNA polymerase I.
  Nucleic Acids Res, 36, 793-802.  
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.  
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.  
19018097 S.M.Soltis, A.E.Cohen, A.Deacon, T.Eriksson, A.González, S.McPhillips, H.Chui, P.Dunten, M.Hollenbeck, I.Mathews, M.Miller, P.Moorhead, R.P.Phizackerley, C.Smith, J.Song, H.van dem Bedem, P.Ellis, P.Kuhn, T.McPhillips, N.Sauter, K.Sharp, I.Tsyba, and G.Wolf (2008).
New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection.
  Acta Crystallogr D Biol Crystallogr, 64, 1210-1221.  
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.  
18669632 T.F.Cheng, X.Hu, A.Gnatt, and P.J.Brooks (2008).
Differential Blocking Effects of the Acetaldehyde-derived DNA Lesion N2-Ethyl-2'-deoxyguanosine on Transcription by Multisubunit and Single Subunit RNA Polymerases.
  J Biol Chem, 283, 27820-27828.  
17179178 C.Zaros, J.F.Briand, Y.Boulard, S.Labarre-Mariotte, M.C.Garcia-Lopez, P.Thuriaux, and F.Navarro (2007).
Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases.
  Nucleic Acids Res, 35, 634-647.  
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.  
18004386 E.Lehmann, F.Brueckner, and P.Cramer (2007).
Molecular basis of RNA-dependent RNA polymerase II activity.
  Nature, 450, 445-449.
PDB codes: 2r92 2r93
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.  
17290000 F.Brueckner, U.Hennecke, T.Carell, and P.Cramer (2007).
CPD damage recognition by transcribing RNA polymerase II.
  Science, 315, 859-862.
PDB codes: 2ja5 2ja6 2ja7 2ja8
17537816 H.Gaillard, R.E.Wellinger, and A.Aguilera (2007).
A new connection of mRNP biogenesis and export with transcription-coupled repair.
  Nucleic Acids Res, 35, 3893-3906.  
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.  
17452638 M.Brulliard, D.Lorphelin, O.Collignon, W.Lorphelin, B.Thouvenot, E.Gothié, S.Jacquenet, V.Ogier, O.Roitel, J.M.Monnez, P.Vallois, F.T.Yen, O.Poch, M.Guenneugues, G.Karcher, P.Oudet, and B.E.Bihain (2007).
Nonrandom variations in human cancer ESTs indicate that mRNA heterogeneity increases during carcinogenesis.
  Proc Natl Acad Sci U S A, 104, 7522-7527.  
17625551 P.Cramer (2007).
Gene transcription: extending the message.
  Nature, 448, 142-143.  
17670940 R.D.Kornberg (2007).
The molecular basis of eukaryotic transcription.
  Proc Natl Acad Sci U S A, 104, 12955-12961.  
17502377 S.Kyzer, K.S.Ha, R.Landick, and M.Palangat (2007).
Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex.
  J Biol Chem, 282, 19020-19028.  
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.  
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.  
16818233 A.J.Jasiak, K.J.Armache, B.Martens, R.P.Jansen, and P.Cramer (2006).
Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model.
  Mol Cell, 23, 71-81.
PDB code: 2ckz
16469698 A.M.Deaconescu, A.L.Chambers, A.J.Smith, B.E.Nickels, A.Hochschild, N.J.Savery, and S.A.Darst (2006).
Structural basis for bacterial transcription-coupled DNA repair.
  Cell, 124, 507-520.
PDB code: 2eyq
17129781 D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, and R.D.Kornberg (2006).
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.
  Cell, 127, 941-954.
PDB codes: 2e2h 2e2i 2e2j 2nvq 2nvs 2nvt 2nvx 2nvy 2nvz 2yu9
17052459 E.Kashkina, M.Anikin, F.Brueckner, R.T.Pomerantz, W.T.McAllister, P.Cramer, and D.Temiakov (2006).
Template misalignment in multisubunit RNA polymerases and transcription fidelity.
  Mol Cell, 24, 257-266.  
16341226 H.Kettenberger, A.Eisenführ, F.Brueckner, M.Theis, M.Famulok, and P.Cramer (2006).
Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs.
  Nat Struct Mol Biol, 13, 44-48.
PDB code: 2b63
16826228 M.Hampsey (2006).
The Pol II initiation complex: finding a place to start.
  Nat Struct Mol Biol, 13, 564-566.  
16873663 N.Zenkin, Y.Yuzenkova, and K.Severinov (2006).
Transcript-assisted transcriptional proofreading.
  Science, 313, 518-520.  
16628221 O.Laptenko, S.S.Kim, J.Lee, M.Starodubtseva, F.Cava, J.Berenguer, X.P.Kong, and S.Borukhov (2006).
pH-dependent conformational switch activates the inhibitor of transcription elongation.
  EMBO J, 25, 2131-2141.
PDB code: 2f23
16765890 P.A.Meyer, P.Ye, M.Zhang, M.H.Suh, and J.Fu (2006).
Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model.
  Structure, 14, 973-982.
PDB code: 2b8k
17147473 P.S.Salgado, M.R.Koivunen, E.V.Makeyev, D.H.Bamford, D.I.Stuart, and J.M.Grimes (2006).
The structure of an RNAi polymerase links RNA silencing and transcription.
  PLoS Biol, 4, e434.
PDB codes: 2j7n 2j7o
17174884 R.Landick, and R.Kornberg (2006).
A long time in the making--the Nobel Prize for RNA polymerase.
  Cell, 127, 1087-1090.  
17052458 R.T.Pomerantz, D.Temiakov, M.Anikin, D.G.Vassylyev, and W.T.McAllister (2006).
A mechanism of nucleotide misincorporation during transcription due to template-strand misalignment.
  Mol Cell, 24, 245-255.  
16621791 S.F.Holmes, T.J.Santangelo, C.K.Cunningham, J.W.Roberts, and D.A.Erie (2006).
Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity.
  J Biol Chem, 281, 18677-18683.  
16900098 T.A.Steitz (2006).
Visualizing polynucleotide polymerase machines at work.
  EMBO J, 25, 3458-3468.  
16524917 V.Trinh, M.F.Langelier, J.Archambault, and B.Coulombe (2006).
Structural perspective on mutations affecting the function of multisubunit RNA polymerases.
  Microbiol Mol Biol Rev, 70, 12-36.  
16600865 W.Yang, J.Y.Lee, and M.Nowotny (2006).
Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
  Mol Cell, 22, 5.  
16094453 B.Coulombe, and M.F.Langelier (2005).
Functional dissection of the catalytic mechanism of mammalian RNA polymerase II.
  Biochem Cell Biol, 83, 497-504.  
15831464 C.Zhang, K.L.Zobeck, and Z.F.Burton (2005).
Human RNA polymerase II elongation in slow motion: role of the TFIIF RAP74 alpha1 helix in nucleoside triphosphate-driven translocation.
  Mol Cell Biol, 25, 3583-3595.  
16360025 D.G.Vassylyev, and I.Artsimovitch (2005).
Tracking RNA polymerase, one step at a time.
  Cell, 123, 977-979.  
16273103 D.G.Vassylyev, V.Svetlov, M.N.Vassylyeva, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, and I.Artsimovitch (2005).
Structural basis for transcription inhibition by tagetitoxin.
  Nat Struct Mol Biol, 12, 1086-1093.
PDB code: 2be5
16167380 D.Temiakov, N.Zenkin, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, E.Kashkina, M.Savkina, S.Zorov, V.Nikiforov, N.Igarashi, N.Matsugaki, S.Wakatsuki, K.Severinov, and D.G.Vassylyev (2005).
Structural basis of transcription inhibition by antibiotic streptolydigin.
  Mol Cell, 19, 655-666.
PDB code: 2a6h
16284617 E.A.Abbondanzieri, W.J.Greenleaf, J.W.Shaevitz, R.Landick, and S.M.Block (2005).
Direct observation of base-pair stepping by RNA polymerase.
  Nature, 438, 460-465.  
15886393 M.F.Langelier, D.Baali, V.Trinh, J.Greenblatt, J.Archambault, and B.Coulombe (2005).
The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II.
  Nucleic Acids Res, 33, 2629-2639.  
16122417 S.Kyzer, J.Zhang, and R.Landick (2005).
Inhibition of RNA polymerase by streptolydigin: no cycling allowed.
  Cell, 122, 494-496.  
16122422 S.Tuske, S.G.Sarafianos, X.Wang, B.Hudson, E.Sineva, J.Mukhopadhyay, J.J.Birktoft, O.Leroy, S.Ismail, A.D.Clark, C.Dharia, A.Napoli, O.Laptenko, J.Lee, S.Borukhov, R.H.Ebright, and E.Arnold (2005).
Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.
  Cell, 122, 541-552.
PDB codes: 1zyr 2cw0
16049026 V.Sosunov, S.Zorov, E.Sosunova, A.Nikolaev, I.Zakeyeva, I.Bass, A.Goldfarb, V.Nikiforov, K.Severinov, and A.Mustaev (2005).
The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase.
  Nucleic Acids Res, 33, 4202-4211.  
16094452 Z.F.Burton, M.Feig, X.Q.Gong, C.Zhang, Y.A.Nedialkov, and Y.Xiong (2005).
NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases.
  Biochem Cell Biol, 83, 486-496.  
15610738 H.Kettenberger, K.J.Armache, and P.Cramer (2004).
Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.
  Mol Cell, 16, 955-965.
PDB codes: 1y1v 1y1w 1y1y 1y77
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.