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PDBsum entry 1s76

Go to PDB code: 
protein dna_rna ligands metals links
Transferase PDB id
1s76
Jmol
Contents
Protein chain
829 a.a. *
DNA/RNA
Ligands
APC
Metals
_MG ×2
* Residue conservation analysis
PDB id:
1s76
Name: Transferase
Title: T7 RNA polymerase alpha beta methylene atp elongation complex
Structure: DNA (5'- d(p Gp Cp Cp Gp Tp Gp Cp Gp Cp Ap Tp Tp Cp Gp Cp Cp Gp Tp G p Tp T)-3'). Chain: t. Engineered: yes. DNA (5'- d(p Tp Tp Tp Ap Cp Gp Tp Tp Gp Cp Gp Cp Ap Cp Gp Gp C)-3'). Chain: n. Engineered: yes.
Source: Synthetic: yes. Other_details: DNA oligomer is synthesized. Other_details: RNA oligomer is synthesized. Enterobacteria phage t7. Organism_taxid: 10760. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.88Å     R-factor:   0.248     R-free:   0.290
Authors: Y.W.Yin,T.A.Steitz
Key ref:
Y.W.Yin and T.A.Steitz (2004). The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell, 116, 393-404. PubMed id: 15016374 DOI: 10.1016/S0092-8674(04)00120-5
Date:
29-Jan-04     Release date:   23-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00573  (RPOL_BPT7) -  T7 RNA polymerase
Seq:
Struc:
 
Seq:
Struc:
883 a.a.
829 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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     transcription, DNA-dependent   1 term 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(04)00120-5 Cell 116:393-404 (2004)
PubMed id: 15016374  
 
 
The structural mechanism of translocation and helicase activity in T7 RNA polymerase.
Y.W.Yin, T.A.Steitz.
 
  ABSTRACT  
 
RNA polymerase functions like a molecular motor that can convert chemical energy into the work of strand separation and translocation along the DNA during transcription. The structures of phage T7 RNA polymerase in an elongation phase substrate complex that includes the incoming nucleoside triphosphate and a pretranslocation product complex that includes the product pyrophosphate (PPi) are described here. These structures and the previously determined posttranslocation elongation complex demonstrate that two enzyme conformations exist during a cycle of single nucleotide addition. One orientation of a five-helix subdomain is stabilized by the phosphates of either the incoming NTP or by the product PPi. A second orientation of this subdomain is stable in their absence and is associated with translocation of the heteroduplex product as well as strand separation of the downstream DNA. We propose that the dissociation of the product PPi after nucleotide addition produces the protein conformational change resulting in translocation and strand separation.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The Oligonucleotides and NTPs Used for Forming the Substrate and Product Complexes(A) The transcription bubble of an elongation phase complex is mimicked by 30 bp of duplex DNA containing a central noncomplementary region; a complementary 17 nt RNA is hybridized to the template DNA in the bubble region.(B) The substrate complex is prepared by addition of a nonhydrolyzable ATP analog, α,β methylene ATP.(C) The product complex is formed by adding a chain terminating nucleotide, 3′ deoxyATP, as well as PP[i].
Figure 8.
Figure 8. The Relative Orientation of the Fingers Helical Subdomain in the Apo-T7 RNAP (“Open” Conformation, Purple), the Posttranslocation (“Semi-Open” Conformation, Gray), and Pretranslocation (“Closed” Conformation, Green)Only two helices of the subdomain are shown. The axis of the O helix rotates by 45° between two open and closed structures and by 22° between the semi-open and closed structures. The template strand (blue) and primer terminus (gray) are shown in the posttranslocation position.
 
  The above figures are reprinted by permission from Cell Press: Cell (2004, 116, 393-404) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22245970 D.Takeshita, and K.Tomita (2012).
Molecular basis for RNA polymerization by Qβ replicase.
  Nat Struct Mol Biol, 19, 229-237.
PDB codes: 3avt 3avu 3avv 3avw 3avx 3avy
  21465580 B.Knobloch, A.Mucha, B.P.Operschall, H.Sigel, M.Jeżowska-Bojczuk, H.Kozłowski, and R.K.Sigel (2011).
Stability and structure of mixed-ligand metal ion complexes that contain Ni2+, Cu2+, or Zn2+, and Histamine, as well as adenosine 5'-triphosphate (ATP4-) or uridine 5'-triphosphate (UTP(4-): an intricate network of equilibria.
  Chemistry, 17, 5393-5403.  
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
21947009 R.Ringel, M.Sologub, Y.I.Morozov, D.Litonin, P.Cramer, and D.Temiakov (2011).
Structure of human mitochondrial RNA polymerase.
  Nature, 478, 269-273.
PDB code: 3spa
21103490 S.Yang, M.Froeyen, E.Lescrinier, P.Marlière, and P.Herdewijn (2011).
3-Phosphono-L-alanine as pyrophosphate mimic for DNA synthesis using HIV-1 reverse transcriptase.
  Org Biomol Chem, 9, 111-119.  
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.
  Structure, 18, 83-93.
PDB codes: 3eyz 3ez5
20533494 A.Giraut, and P.Herdewijn (2010).
Influence of the linkage between leaving group and nucleoside on substrate efficiency for incorporation in DNA catalyzed by reverse transcriptase.
  Chembiochem, 11, 1399-1403.  
20097909 A.Giraut, X.P.Song, M.Froeyen, P.Marlière, and P.Herdewijn (2010).
Iminodiacetic-phosphoramidates as metabolic prototypes for diversifying nucleic acid polymerization in vivo.
  Nucleic Acids Res, 38, 2541-2550.  
21071662 B.Pan, Y.Xiong, and T.A.Steitz (2010).
How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA.
  Science, 330, 937-940.
PDB codes: 3ouy 3ov7 3ova 3ovb 3ovs
20301166 C.Chou, D.D.Young, and A.Deiters (2010).
Photocaged t7 RNA polymerase for the light activation of transcription and gene function in pro- and eukaryotic cells.
  Chembiochem, 11, 972-977.  
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
20152146 J.D.Pata, and J.Jaeger (2010).
Molecular machines and targeted molecular dynamics: DNA in motion.
  Structure, 18, 4-6.  
20376302 K.Singh, B.Marchand, K.A.Kirby, E.Michailidis, and S.G.Sarafianos (2010).
Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.
  Viruses, 2, 606-638.  
19665597 M.Götte, J.W.Rausch, B.Marchand, S.Sarafianos, and S.F.Le Grice (2010).
Reverse transcriptase in motion: conformational dynamics of enzyme-substrate interactions.
  Biochim Biophys Acta, 1804, 1202-1212.  
20111609 M.Yokoyama, H.Mori, and H.Sato (2010).
Allosteric regulation of HIV-1 reverse transcriptase by ATP for nucleotide selection.
  PLoS One, 5, e8867.  
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
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.  
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.  
19307179 D.Nayak, Q.Guo, and R.Sousa (2009).
A promoter recognition mechanism common to yeast mitochondrial and phage t7 RNA polymerases.
  J Biol Chem, 284, 13641-13647.  
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.  
19486663 L.Mollazadeh-Beidokhti, F.Mohammad-Rafiee, and H.Schiessel (2009).
Active nucleosome displacement: a theoretical approach.
  Biophys J, 96, 4387-4398.  
19389406 L.Wang, S.Broyde, and Y.Zhang (2009).
Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase.
  J Mol Biol, 389, 787-796.  
19300826 R.N.Veedu, B.Vester, and J.Wengel (2009).
Efficient enzymatic synthesis of LNA-modified DNA duplexes using KOD DNA polymerase.
  Org Biomol Chem, 7, 1404-1409.  
19383448 Y.R.Yamada, and C.S.Peskin (2009).
A look-ahead model for the elongation dynamics of transcription.
  Biophys J, 96, 3015-3031.  
19837034 Y.S.Lee, W.D.Kennedy, and Y.W.Yin (2009).
Structural insight into processive human mitochondrial DNA synthesis and disease-related polymerase mutations.
  Cell, 139, 312-324.
PDB codes: 3ikl 3ikm
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.  
18827944 A.Mucha, B.Knobloch, M.Jezowska-Bojczuk, H.Kozłowski, and R.K.Sigel (2008).
Effect of the ribose versus 2'-deoxyribose residue on the metal ion-binding properties of purine nucleotides.
  Dalton Trans, (), 5368-5377.  
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
18177750 G.Martin, S.Doublié, and W.Keller (2008).
Determinants of substrate specificity in RNA-dependent nucleotidyl transferases.
  Biochim Biophys Acta, 1779, 206-216.  
18536012 H.J.Woo, Y.Liu, and R.Sousa (2008).
Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes.
  Proteins, 73, 1021-1036.  
  18268843 K.K.Ng, J.J.Arnold, and C.E.Cameron (2008).
Structure-function relationships among RNA-dependent RNA polymerases.
  Curr Top Microbiol Immunol, 320, 137-156.  
18410247 K.M.Herbert, W.J.Greenleaf, and S.M.Block (2008).
Single-molecule studies of RNA polymerase: motoring along.
  Annu Rev Biochem, 77, 149-176.  
18362338 K.S.Murakami, E.K.Davydova, and L.B.Rothman-Denes (2008).
X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase.
  Proc Natl Acad Sci U S A, 105, 5046-5051.
PDB code: 2po4
19061645 M.L.Gleghorn, E.K.Davydova, L.B.Rothman-Denes, and K.S.Murakami (2008).
Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.
  Mol Cell, 32, 707-717.
PDB codes: 3c2p 3c3l 3c46
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.  
18167548 M.Pandey, S.S.Patel, and A.Gabriel (2008).
Kinetic pathway of pyrophosphorolysis by a retrotransposon reverse transcriptase.
  PLoS ONE, 3, e1389.  
18708471 P.Thomen, P.J.Lopez, U.Bockelmann, J.Guillerez, M.Dreyfus, and F.Heslot (2008).
T7 RNA polymerase studied by force measurements varying cofactor concentration.
  Biophys J, 95, 2423-2433.  
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.  
17223130 A.A.Thompson, R.A.Albertini, and O.B.Peersen (2007).
Stabilization of poliovirus polymerase by NTP binding and fingers-thumb interactions.
  J Mol Biol, 366, 1459-1474.
PDB codes: 2ily 2ilz 2im0 2im1 2im2 2im3
17611604 A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lázaro, M.de Vega, L.Blanco, M.Salas, and T.A.Steitz (2007).
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.
  EMBO J, 26, 3494-3505.
PDB codes: 2py5 2pyj 2pyl 2pzs
17145704 B.Marchand, E.P.Tchesnokov, and M.Götte (2007).
The pyrophosphate analogue foscarnet traps the pre-translocational state of HIV-1 reverse transcriptase in a Brownian ratchet model of polymerase translocation.
  J Biol Chem, 282, 3337-3346.  
17360513 C.Castro, E.Smidansky, K.R.Maksimchuk, J.J.Arnold, V.S.Korneeva, M.Götte, W.Konigsberg, and C.E.Cameron (2007).
Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases.
  Proc Natl Acad Sci U S A, 104, 4267-4272.  
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
17580086 D.Nayak, Q.Guo, and R.Sousa (2007).
Functional architecture of T7 RNA polymerase transcription complexes.
  J Mol Biol, 371, 490-500.  
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.  
17259182 K.Singh, A.Srivastava, S.S.Patel, and M.J.Modak (2007).
Participation of the fingers subdomain of Escherichia coli DNA polymerase I in the strand displacement synthesis of DNA.
  J Biol Chem, 282, 10594-10604.  
17693436 M.Kimoto, T.Mitsui, Y.Harada, A.Sato, S.Yokoyama, and I.Hirao (2007).
Fluorescent probing for RNA molecules by an unnatural base-pair system.
  Nucleic Acids Res, 35, 5360-5369.  
17625551 P.Cramer (2007).
Gene transcription: extending the message.
  Nature, 448, 142-143.  
17400246 P.R.Meyer, W.Rutvisuttinunt, S.E.Matsuura, A.G.So, and W.A.Scott (2007).
Stable complexes formed by HIV-1 reverse transcriptase at distinct positions on the primer-template controlled by binding deoxynucleoside triphosphates or foscarnet.
  J Mol Biol, 369, 41-54.  
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.  
16498624 C.H.Schein, D.E.Volk, N.Oezguen, and A.Paul (2006).
Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses.
  Proteins, 63, 719-726.  
16317791 D.W.Heinz, M.S.Weiss, and K.U.Wendt (2006).
Biomacromolecular interactions, assemblies and machines: a structural view.
  Chembiochem, 7, 203-208.  
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.  
16415021 E.P.Tchesnokov, C.Gilbert, G.Boivin, and M.Götte (2006).
Role of helix P of the human cytomegalovirus DNA polymerase in resistance and hypersusceptibility to the antiviral drug foscarnet.
  J Virol, 80, 1440-1450.  
16907127 H.J.Woo (2006).
Analytical theory of the nonequilibrium spatial distribution of RNA polymerase translocations.
  Phys Rev E Stat Nonlin Soft Matter Phys, 74, 011907.  
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.  
16843892 K.H.Choi, A.Gallei, P.Becher, and M.G.Rossmann (2006).
The structure of bovine viral diarrhea virus RNA-dependent RNA polymerase and its amino-terminal domain.
  Structure, 14, 1107-1113.
PDB code: 2cjq
17051158 K.Tomita, R.Ishitani, S.Fukai, and O.Nureki (2006).
Complete crystallographic analysis of the dynamics of CCA sequence addition.
  Nature, 443, 956-960.
PDB codes: 2dr5 2dr7 2dr8 2dr9 2dra 2drb 2dvi
16689640 L.Bai, T.J.Santangelo, and M.D.Wang (2006).
Single-molecule analysis of RNA polymerase transcription.
  Annu Rev Biophys Biomol Struct, 35, 343-360.  
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.  
16537373 V.R.Tadigotla, D.O Maoiléidigh, A.M.Sengupta, V.Epshtein, R.H.Ebright, E.Nudler, and A.E.Ruckenstein (2006).
Thermodynamic and kinetic modeling of transcriptional pausing.
  Proc Natl Acad Sci U S A, 103, 4439-4444.  
17005565 V.S.Anand, and S.S.Patel (2006).
Transient state kinetics of transcription elongation by T7 RNA polymerase.
  J Biol Chem, 281, 35677-35685.  
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.  
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.  
15574519 F.J.Blocker, G.Mohr, L.H.Conlan, L.Qi, M.Belfort, and A.M.Lambowitz (2005).
Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase.
  RNA, 11, 14-28.  
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.
  Cell, 120, 183-193.  
15878882 J.J.Arnold, M.Vignuzzi, J.K.Stone, R.Andino, and C.E.Cameron (2005).
Remote site control of an active site fidelity checkpoint in a viral RNA-dependent RNA polymerase.
  J Biol Chem, 280, 25706-25716.  
16304655 N.Carrasco, J.Caton-Williams, G.Brandt, S.Wang, and Z.Huang (2005).
Efficient enzymatic synthesis of phosphoroselenoate RNA by using adenosine 5'-(alpha-P-seleno)triphosphate.
  Angew Chem Int Ed Engl, 45, 94-97.  
15903965 P.Thomen, P.J.Lopez, and F.Heslot (2005).
Unravelling the mechanism of RNA-polymerase forward motion by using mechanical force.
  Phys Rev Lett, 94, 128102.  
16140780 R.Chen, M.Yokoyama, H.Sato, C.Reilly, and L.M.Mansky (2005).
Human immunodeficiency virus mutagenesis during antiviral therapy: impact of drug-resistant reverse transcriptase and nucleoside and nonnucleoside reverse transcriptase inhibitors on human immunodeficiency virus type 1 mutation frequencies.
  J Virol, 79, 12045-12057.  
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.  
15016373 D.Temiakov, V.Patlan, M.Anikin, W.T.McAllister, S.Yokoyama, and D.G.Vassylyev (2004).
Structural basis for substrate selection by t7 RNA polymerase.
  Cell, 116, 381-391.
PDB code: 1s0v
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
15537538 K.D.Westover, D.A.Bushnell, and R.D.Kornberg (2004).
Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
  Cell, 119, 481-489.
PDB codes: 1r9s 1r9t 1twa 1twc 1twf 1twg 1twh
15295603 K.Tomita, S.Fukai, R.Ishitani, T.Ueda, N.Takeuchi, D.G.Vassylyev, and O.Nureki (2004).
Structural basis for template-independent RNA polymerization.
  Nature, 430, 700-704.
PDB code: 1vfg
15231739 M.L.Duquette, P.Handa, J.A.Vincent, A.F.Taylor, and N.Maizels (2004).
Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA.
  Genes Dev, 18, 1618-1629.  
15574497 N.N.Batada, K.D.Westover, D.A.Bushnell, M.Levitt, and R.D.Kornberg (2004).
Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center.
  Proc Natl Acad Sci U S A, 101, 17361-17364.  
15016367 R.Landick (2004).
Active-site dynamics in RNA polymerases.
  Cell, 116, 351-353.  
15102443 T.A.Steitz (2004).
The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase.
  Curr Opin Struct Biol, 14, 4-9.  
15262972 V.Svetlov, D.G.Vassylyev, and I.Artsimovitch (2004).
Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase.
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