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PDBsum entry 2e2h
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protein dna_rna ligands metals Protein-protein interface(s) links
Transcription,transferase/DNA-RNA hybrid PDB id
2e2h

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
1398 a.a. *
1096 a.a. *
266 a.a. *
193 a.a. *
83 a.a. *
133 a.a. *
119 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
DNA/RNA
Ligands
GTP
Metals
_MG ×2
_ZN ×8
* Residue conservation analysis
PDB id:
2e2h
Name: Transcription,transferase/DNA-RNA hybrid
Title: RNA polymerase ii elongation complex at 5 mm mg2+ with gtp
Structure: 5'-r( Ap Up Cp Gp Ap Gp Ap Gp Gp A)-3'. Chain: r. Engineered: yes. 28-mer DNA template strand. Chain: t. Engineered: yes. 5'-d( Cp Tp Gp Cp Tp Tp Ap Tp Cp Gp Gp Tp Ap G)-3'. Chain: n. Engineered: yes.
Source: Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: delta-rpb4. Strain: delta-rpb4
Biol. unit: 13mer (from PQS)
Resolution:
3.95Å     R-factor:   0.294     R-free:   0.368
Authors: D.Wang,D.A.Bushnell,K.D.Westover,C.D.Kaplan,R.D.Kornberg
Key ref:
D.Wang et al. (2006). Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell, 127, 941-954. PubMed id: 17129781 DOI: 10.1016/j.cell.2006.11.023
Date:
14-Nov-06     Release date:   12-Dec-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1733 a.a.
1398 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1224 a.a.
1096 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		215 a.a.
193 a.a.
Protein chain
Pfam   ArchSchema ?
P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		155 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		146 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		70 a.a.
46 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  A-U-C-G-A-G-A-G-G-A 10 bases
  C-T-A-C-C-G-A-T-A-A-G-C-A-G-A-C-G-C-T-C-C-T-C-T-C-G-A-T 28 bases
  C-T-G-C-T-T-A-T-C-G-G-T-A-G 14 bases

 Enzyme reactions 
   Enzyme class: Chains A, B, C, E, F, H, I, J, K, L: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
RNA(n)
 + ribonucleoside 5'-triphosphate
 = RNA(n+1)
 + diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/j.cell.2006.11.023 Cell 127:941-954 (2006)
PubMed id: 17129781  
 
 
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.
D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, R.D.Kornberg.
 
  ABSTRACT  
 
New structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues. A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. A and E Sites in the Pol II Transcribing Complex 		Figure 5.
Figure 5. Proposed Role of His1085 in Phosphodiester Bond Formation
 
  The above figures are reprinted by permission from Cell Press: Cell (2006, 127, 941-954) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23151482 S.Sainsbury, J.Niesser, and P.Cramer (2013).
Structure and function of the initially transcribing RNA polymerase II-TFIIB complex.
  Nature, 493, 437-440.
PDB codes: 4bbr 4bbs
22820989 M.W.Kellinger, C.X.Song, J.Chong, X.Y.Lu, C.He, and D.Wang (2012).
5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription.
  Nat Struct Mol Biol, 19, 831-833.  
21346759 A.C.Cheung, and P.Cramer (2011).
Structural basis of RNA polymerase II backtracking, arrest and reactivation.
  Nature, 471, 249-253.
PDB codes: 3po2 3po3
21263028 B.Albert, I.Léger-Silvestre, C.Normand, M.K.Ostermaier, J.Pérez-Fernández, K.I.Panov, J.C.Zomerdijk, P.Schultz, and O.Gadal (2011).
RNA polymerase I-specific subunits promote polymerase clustering to enhance the rRNA gene transcription cycle.
  J Cell Biol, 192, 277-293.  
21265743 H.Heindl, P.Greenwell, N.Weingarten, T.Kiss, G.Terstyanszky, and R.O.Weinzierl (2011).
Cation-Ï€ interactions induce kinking of a molecular hinge in the RNA polymerase bridge-helix domain.
  Biochem Soc Trans, 39, 31-35.  
21183467 H.Zhao, Y.Yang, and Y.Zhou (2011).
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.
  Nucleic Acids Res, 39, 3017-3025.  
21321236 M.L.Gleghorn, E.K.Davydova, R.Basu, L.B.Rothman-Denes, and K.S.Murakami (2011).
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
  Proc Natl Acad Sci U S A, 108, 3566-3571.
PDB codes: 3q0a 3q22 3q23 3q24
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.  
20598112 C.D.Kaplan (2010).
The architecture of RNA polymerase fidelity.
  BMC Biol, 8, 85.  
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.  
20637414 D.Elmlund, R.Davis, and H.Elmlund (2010).
Ab initio structure determination from electron microscopic images of single molecules coexisting in different functional states.
  Structure, 18, 777-786.  
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.  
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
19940126 G.A.Kassavetis, P.Prakash, and E.Shim (2010).
The C53/C37 subcomplex of RNA polymerase III lies near the active site and participates in promoter opening.
  J Biol Chem, 285, 2695-2706.  
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.  
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.  
20367031 L.A.Selth, S.Sigurdsson, and J.Q.Svejstrup (2010).
Transcript Elongation by RNA Polymerase II.
  Annu Rev Biochem, 79, 271-293.  
  21326898 N.Miropolskaya, V.Nikiforov, S.KlimaÅ¡auskas, I.Artsimovitch, and A.Kulbachinskiy (2010).
Modulation of RNA polymerase activity through trigger loop folding.
  Transcr, 1, 89-94.  
  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
20482321 P.Cramer (2010).
Towards molecular systems biology of gene transcription and regulation.
  Biol Chem, 391, 731-735.  
21148772 P.Gong, and O.B.Peersen (2010).
Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase.
  Proc Natl Acad Sci U S A, 107, 22505-22510.
PDB codes: 3ol6 3ol7 3ol8 3ol9 3ola 3olb
21114873 P.P.Hein, and R.Landick (2010).
The bridge helix coordinates movements of modules in RNA polymerase.
  BMC Biol, 8, 141.  
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.  
  21326901 S.De Carlo, S.C.Lin, D.J.Taatjes, and A.Hoenger (2010).
Molecular basis of transcription initiation in Archaea.
  Transcr, 1, 103-111.  
20040576 S.Grünberg, C.Reich, M.E.Zeller, M.S.Bartlett, and M.Thomm (2010).
Rearrangement of the RNA polymerase subunit H and the lower jaw in archaeal elongation complexes.
  Nucleic Acids Res, 38, 1950-1963.  
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
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.  
20459653 Y.Yuzenkova, A.Bochkareva, V.R.Tadigotla, M.Roghanian, S.Zorov, K.Severinov, and N.Zenkin (2010).
Stepwise mechanism for transcription fidelity.
  BMC Biol, 8, 54.  
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.  
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
19151724 C.Castro, E.D.Smidansky, J.J.Arnold, K.R.Maksimchuk, I.Moustafa, A.Uchida, M.Götte, W.Konigsberg, and C.E.Cameron (2009).
Nucleic acid polymerases use a general acid for nucleotidyl transfer.
  Nat Struct Mol Biol, 16, 212-218.  
19910183 C.E.Cameron, I.M.Moustafa, and J.J.Arnold (2009).
Dynamics: the missing link between structure and function of the viral RNA-dependent RNA polymerase?
  Curr Opin Struct Biol, 19, 768-774.  
20004159 C.W.Carter (2009).
E pluribus tres: the 2009 nobel prize in chemistry.
  Structure, 17, 1558-1561.  
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.  
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 3gtl 3gtm 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.  
19647516 H.Saeki, and J.Q.Svejstrup (2009).
Stability, flexibility, and dynamic interactions of colliding RNA polymerase II elongation complexes.
  Mol Cell, 35, 191-205.  
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
19398005 M.Kireeva, Y.A.Nedialkov, X.Q.Gong, C.Zhang, Y.Xiong, W.Moon, Z.F.Burton, and M.Kashlev (2009).
Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase.
  Methods, 48, 333-345.  
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.  
19945377 M.Sologub, D.Litonin, M.Anikin, A.Mustaev, and D.Temiakov (2009).
TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase.
  Cell, 139, 934-944.  
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.  
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
  20046924 R.C.Todd, and S.J.Lippard (2009).
Inhibition of transcription by platinum antitumor compounds.
  Metallomics, 1, 280-291.  
19278646 R.Landick (2009).
Functional divergence in the growing family of RNA polymerases.
  Structure, 17, 323-325.  
19452133 W.Hwang, and M.J.Lang (2009).
Mechanical design of translocating motor proteins.
  Cell Biochem Biophys, 54, 11-22.  
19074952 Y.H.Lo, K.L.Tsai, Y.J.Sun, W.T.Chen, C.Y.Huang, and C.D.Hsiao (2009).
The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA.
  Nucleic Acids Res, 37, 804-814.
PDB codes: 2vye 2vyf
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.  
18854351 A.Dimitri, J.A.Burns, S.Broyde, and D.A.Scicchitano (2008).
Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
  Nucleic Acids Res, 36, 6459-6471.  
18555749 A.Dimitri, L.Jia, V.Shafirovich, N.E.Geacintov, S.Broyde, and D.A.Scicchitano (2008).
Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase.
  DNA Repair (Amst), 7, 1276-1288.  
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
18468900 F.Werner (2008).
Structural evolution of multisubunit RNA polymerases.
  Trends Microbiol, 16, 247-250.  
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.  
18579768 K.S.Lovejoy, R.C.Todd, S.Zhang, M.S.McCormick, J.A.D'Aquino, J.T.Reardon, A.Sancar, K.M.Giacomini, and S.J.Lippard (2008).
cis-Diammine(pyridine)chloroplatinum(II), a monofunctional platinum(II) antitumor agent: Uptake, structure, function, and prospects.
  Proc Natl Acad Sci U S A, 105, 8902-8907.
PDB code: 3co3
17849388 K.Wittayanarakul, S.Hannongbua, and M.Feig (2008).
Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors.
  J Comput Chem, 29, 673-685.  
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.  
18384908 M.Kwapisz, F.Beckouët, and P.Thuriaux (2008).
Early evolution of eukaryotic DNA-dependent RNA polymerases.
  Trends Genet, 24, 211-215.  
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.  
18280161 S.Borukhov, and E.Nudler (2008).
RNA polymerase: the vehicle of transcription.
  Trends Microbiol, 16, 126-134.  
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.  
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.  
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.  
18679430 V.Svetlov, and E.Nudler (2008).
Jamming the ratchet of transcription.
  Nat Struct Mol Biol, 15, 777-779.  
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
17526498 E.Kashkina, M.Anikin, F.Brueckner, E.Lehmann, S.N.Kochetkov, W.T.McAllister, P.Cramer, and D.Temiakov (2007).
Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site.
  J Biol Chem, 282, 21578-21582.  
18233933 E.Zamora-Sillero, A.V.Shapovalov, and F.J.Esteban (2007).
Formation, control, and dynamics of N localized structures in the Peyrard-Bishop model.
  Phys Rev E Stat Nonlin Soft Matter Phys, 76, 066603.  
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.  
17553959 N.Alic, N.Ayoub, E.Landrieux, E.Favry, P.Baudouin-Cornu, M.Riva, and C.Carles (2007).
Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription.
  Proc Natl Acad Sci U S A, 104, 10400-10405.  
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.  
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.  
17174884 R.Landick, and R.Kornberg (2006).
A long time in the making--the Nobel Prize for RNA polymerase.
  Cell, 127, 1087-1090.  
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 codes are shown on the right.

 

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