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PDBsum entry 1pqv

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protein metals links
Transferase/transcription PDB id
1pqv
Jmol
Contents
Protein chains
1409 a.a.* *
1103 a.a.* *
266 a.a.* *
135 a.a.* *
214 a.a.* *
84 a.a.* *
169 a.a.* *
133 a.a.* *
119 a.a.* *
65 a.a.* *
114 a.a.* *
46 a.a.* *
174 a.a.* *
Metals
_ZN ×9
_MG
* Residue conservation analysis
* C-alpha coords only
PDB id:
1pqv
Name: Transferase/transcription
Title: RNA polymerase ii-tfiis complex
Structure: DNA-directed RNA polymerase ii largest subunit. Chain: a. Synonym: b220. DNA-directed RNA polymerase ii 140 kda polypeptide. Chain: b. Synonym: b150. RNA polymerase ii subunit 2. DNA-directed RNA polymerase ii 45 kda polypeptide.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932
Biol. unit: 30mer (from PQS)
Resolution:
3.80Å     R-factor:   not given    
Authors: H.Kettenberger,K.-J.Armache,P.Cramer
Key ref:
H.Kettenberger et al. (2003). Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell, 114, 347-357. PubMed id: 12914699 DOI: 10.1016/S0092-8674(03)00598-1
Date:
19-Jun-03     Release date:   19-Aug-03    
 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.
1409 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.
1103 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 ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4
Seq:
Struc:
221 a.a.
135 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 ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7
Seq:
Struc:
171 a.a.
169 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.
Protein chain
Pfam   ArchSchema ?
P07273  (TFS2_YEAST) -  Transcription elongation factor S-II
Seq:
Struc:
309 a.a.
174 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 29 residue positions (black crosses)

 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
+ 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   8 terms 
  Biological process     transcription, RNA-dependent   29 terms 
  Biochemical function     RNA polymerase II activity     23 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(03)00598-1 Cell 114:347-357 (2003)
PubMed id: 12914699  
 
 
Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage.
H.Kettenberger, K.J.Armache, P.Cramer.
 
  ABSTRACT  
 
The transcription elongation factor TFIIS induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II. We have diffused TFIIS into Pol II crystals and derived a model of the Pol II-TFIIS complex from X-ray diffraction data to 3.8 A resolution. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 A. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active center. Our results support the idea that Pol II contains a single tunable active site for RNA polymerization and cleavage, in contrast to DNA polymerases with two separate active sites for DNA polymerization and cleavage.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Model of a Pol II-TFIIS-Nucleic Acid Complex(A) Side view. The DNA template strand (blue) and the RNA transcript (red) were placed onto the model of Figure 2B according to their location in the elongation complex structure (Gnatt et al., 2001). The Rpb2 protrusion, fork, and external domains were omitted for clarity. The presumed location of backtracked RNA is indicated as a dashed red ribbon. The arrows indicate movement of Pol II relative to the nucleic acids.(B) Cut-away view of the model in (A) from the front. TFIIS and nucleic acids are shown as ribbon models on the molecular surface of Pol II, which is cut along the vertical slice plane indicated in (A). The presumed path of backtracked RNA through the restricted pore is drawn as a dashed red ribbon. The backtracked portion of RNA would be cut at the active site during TFIIS-induced RNA cleavage.(C) Proximity of the TFIIS acidic hairpin to the potential scissile RNA phosphodiester bond. The view is as in (A). RNA was placed according to the location in the Pol II elongation complex structure (Gnatt et al., 2001), and is shown as a stick model with phosphorous atoms highlighted as blue spheres. The black arrow indicates the direction of a possible S[N]2-type nucleophilic in-line attack of the scissile bond (blue).
Figure 5.
Figure 5. TFIIS-Induced Structural Changes in Pol II(A) Local remodeling of the Pol II active center. Structural elements of the active center in the Pol II-TFIIS complex are shown as ribbons in different colors. The corresponding elements in the free 12-subunit Pol II structure are shown superimposed in beige. In the Pol II-TFIIS complex, the trigger loop (blue) and fork loop 2 (pink) are folded, parts of the bridge helix (cyan) are shifted upward, and switches 1 and 2 (red and purple, respectively) moved outward. The DNA template strand (blue) and product RNA (red) have been placed according to the Pol II elongation complex structure (Gnatt et al., 2001). A pink sphere marks the location of metal ion A (Cramer et al. 2000 and Cramer et al. 2001).(B) Opening of the Pol II crevice and insertion of the TFIIS linker. Detailed view of the TFIIS linker (yellow) passing through the crevice (magenta). The location of the two crevice-forming elements in free Pol II is shown in beige. The view is from the bottom, as in Figure 2 and Figure 3.(C–E) Global repositioning of the Pol II mobile mass. In (C), regions of the model in Figure 2B that are repositioned upon TFIIS binding (mobile mass) are highlighted in magenta. In (D), changes in the mobile mass between free Pol II (beige) and the Pol II-TFIIS complex (magenta) are shown. The models were superimposed based on the unchanged regions in the Pol II core module (Cramer et al., 2001). Arrows indicate the direction and magnitude of movements at outer positions. The location of the incoming DNA duplex during transcription elongation is indicated as a dashed blue circle. In (E), Pol II regions contributing to the mobile mass are shown. Subunits are colored according to the color code used previously (Armache et al. 2003; Cramer et al. 2000 and Cramer et al. 2001).
 
  The above figures are reprinted by permission from Cell Press: Cell (2003, 114, 347-357) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
  21417597 A.Y.Park, and C.V.Robinson (2011).
Protein-nucleic acid complexes and the role of mass spectrometry in their structure determination.
  Crit Rev Biochem Mol Biol, 46, 152-164.  
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
21127351 M.Cojocaru, A.Bouchard, P.Cloutier, J.J.Cooper, K.Varzavand, D.H.Price, and B.Coulombe (2011).
Transcription Factor IIS Cooperates with the E3 Ligase UBR5 to Ubiquitinate the CDK9 Subunit of the Positive Transcription Elongation Factor B.
  J Biol Chem, 286, 5012-5022.  
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.  
20367031 L.A.Selth, S.Sigurdsson, and J.Q.Svejstrup (2010).
Transcript Elongation by RNA Polymerase II.
  Annu Rev Biochem, 79, 271-293.  
20482321 P.Cramer (2010).
Towards molecular systems biology of gene transcription and regulation.
  Biol Chem, 391, 731-735.  
20417599 S.Sigurdsson, A.B.Dirac-Svejstrup, and J.Q.Svejstrup (2010).
Evidence that transcript cleavage is essential for RNA polymerase II transcription and cell viability.
  Mol Cell, 38, 202-210.  
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.  
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.  
18830703 D.S.Gilmour (2009).
Promoter proximal pausing on genes in metazoans.
  Chromosoma, 118, 1.  
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.  
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.  
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
19148274 M.D.Blankschien, K.Potrykus, E.Grace, A.Choudhary, D.Vinella, M.Cashel, and C.Herman (2009).
TraR, a homolog of a RNAP secondary channel interactor, modulates transcription.
  PLoS Genet, 5, e1000345.  
19411170 T.W.Sikorski, and S.Buratowski (2009).
The basal initiation machinery: beyond the general transcription factors.
  Curr Opin Cell Biol, 21, 344-351.  
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
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.  
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.  
18627464 P.Uzureau, J.P.Daniels, D.Walgraffe, B.Wickstead, E.Pays, K.Gull, and L.Vanhamme (2008).
Identification and characterization of two trypanosome TFIIS proteins exhibiting particular domain architectures and differential nuclear localizations.
  Mol Microbiol, 69, 1121-1136.  
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.  
18628399 Y.Ghavi-Helm, M.Michaut, J.Acker, J.C.Aude, P.Thuriaux, M.Werner, and J.Soutourina (2008).
Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription.
  Genes Dev, 22, 1934-1947.  
17951384 A.Hochschild (2007).
Gene-specific regulation by a transcript cleavage factor: facilitating promoter escape.
  J Bacteriol, 189, 8769-8771.  
17901206 B.Guglielmi, J.Soutourina, C.Esnault, and M.Werner (2007).
TFIIS elongation factor and Mediator act in conjunction during transcription initiation in vivo.
  Proc Natl Acad Sci U S A, 104, 16062-16067.  
17913884 B.Kim, A.I.Nesvizhskii, P.G.Rani, S.Hahn, R.Aebersold, and J.A.Ranish (2007).
The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes.
  Proc Natl Acad Sci U S A, 104, 16068-16073.  
18160037 C.D.Kuhn, S.R.Geiger, S.Baumli, M.Gartmann, J.Gerber, S.Jennebach, T.Mielke, H.Tschochner, R.Beckmann, and P.Cramer (2007).
Functional architecture of RNA polymerase I.
  Cell, 131, 1260-1272.
PDB code: 2rf4
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
17697097 F.Werner (2007).
Structure and function of archaeal RNA polymerases.
  Mol Microbiol, 65, 1395-1404.  
17535246 H.Koyama, T.Ito, T.Nakanishi, and K.Sekimizu (2007).
Stimulation of RNA polymerase II transcript cleavage activity contributes to maintain transcriptional fidelity in yeast.
  Genes Cells, 12, 547-559.  
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.  
17180359 M.A.Moreno-Risueno, M.Martínez, J.Vicente-Carbajosa, and P.Carbonero (2007).
The family of DOF transcription factors: from green unicellular algae to vascular plants.
  Mol Genet Genomics, 277, 379-390.  
17336362 S.G.Cresawn, C.Prins, D.R.Latner, and R.C.Condit (2007).
Mapping and phenotypic analysis of spontaneous isatin-beta-thiosemicarbazone resistant mutants of vaccinia virus.
  Virology, 363, 319-332.  
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.  
17584298 Y.Yamaguchi, T.Mura, S.Chanarat, S.Okamoto, and H.Handa (2007).
Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity.
  Genes Cells, 12, 863-875.  
  16511259 A.A.Perederina, M.N.Vassylyeva, I.A.Berezin, V.Svetlov, I.Artsimovitch, and D.G.Vassylyev (2006).
Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors GreB from Escherichia coli and Gfh1 from Thermus thermophilus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 44-46.  
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
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
16819517 G.Miller, and S.Hahn (2006).
A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex.
  Nat Struct Mol Biol, 13, 603-610.  
16421445 H.Kettenberger, and P.Cramer (2006).
Fluorescence detection of nucleic acids and proteins in multi-component crystals.
  Acta Crystallogr D Biol Crystallogr, 62, 146-150.  
16298991 J.Symersky, A.Perederina, M.N.Vassylyeva, V.Svetlov, I.Artsimovitch, and D.G.Vassylyev (2006).
Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors.
  J Biol Chem, 281, 1309-1312.
PDB code: 2eul
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.  
16630816 M.Guermah, V.B.Palhan, A.J.Tackett, B.T.Chait, and R.G.Roeder (2006).
Synergistic functions of SII and p300 in productive activator-dependent transcription of chromatin templates.
  Cell, 125, 275-286.  
16492753 N.K.Nesser, D.O.Peterson, and D.K.Hawley (2006).
RNA polymerase II subunit Rpb9 is important for transcriptional fidelity in vivo.
  Proc Natl Acad Sci U S A, 103, 3268-3273.  
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
17146456 P.Cramer (2006).
Deciphering the RNA polymerase II structure: a personal perspective.
  Nat Struct Mol Biol, 13, 1042-1044.  
17174884 R.Landick, and R.Kornberg (2006).
A long time in the making--the Nobel Prize for RNA polymerase.
  Cell, 127, 1087-1090.  
16648643 R.N.Fish, M.L.Ammerman, J.K.Davie, B.F.Lu, C.Pham, L.Howe, A.S.Ponticelli, and C.M.Kane (2006).
Genetic interactions between TFIIF and TFIIS.
  Genetics, 173, 1871-1884.  
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.
  Structure, 14, 1691-1700.  
17030604 S.Li, B.Ding, R.Chen, C.Ruggiero, and X.Chen (2006).
Evidence that the transcription elongation function of Rpb9 is involved in transcription-coupled DNA repair in Saccharomyces cerevisiae.
  Mol Cell Biol, 26, 9430-9441.  
16687245 T.Cremer, M.Cremer, S.Dietzel, S.Müller, I.Solovei, and S.Fakan (2006).
Chromosome territories--a functional nuclear landscape.
  Curr Opin Cell Biol, 18, 307-316.  
16581793 T.Ito, N.Arimitsu, M.Takeuchi, N.Kawamura, M.Nagata, K.Saso, N.Akimitsu, H.Hamamoto, S.Natori, A.Miyajima, and K.Sekimizu (2006).
Transcription elongation factor S-II is required for definitive hematopoiesis.
  Mol Cell Biol, 26, 3194-3203.  
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.  
16648364 Y.Ling, A.J.Smith, and G.T.Morgan (2006).
A sequence motif conserved in diverse nuclear proteins identifies a protein interaction domain utilised for nuclear targeting by human TFIIS.
  Nucleic Acids Res, 34, 2219-2229.  
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.  
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
15767671 D.M.Prather, E.Larschan, and F.Winston (2005).
Evidence that the elongation factor TFIIS plays a role in transcription initiation at GAL1 in Saccharomyces cerevisiae.
  Mol Cell Biol, 25, 2650-2659.  
15916593 E.P.Geiduschek, and M.Ouhammouch (2005).
Archaeal transcription and its regulators.
  Mol Microbiol, 56, 1397-1407.  
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.  
15542547 J.L.Knight, V.Mekler, J.Mukhopadhyay, R.H.Ebright, and R.M.Levy (2005).
Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability.
  Biophys J, 88, 925-938.  
15629721 K.Adelman, M.T.Marr, J.Werner, A.Saunders, Z.Ni, E.D.Andrulis, and J.T.Lis (2005).
Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS.
  Mol Cell, 17, 103-112.  
15743411 K.Hayashi, T.Watanabe, A.Tanaka, T.Furumoto, C.Sato-Tsuchiya, M.Kimura, M.Yokoi, A.Ishihama, F.Hanaoka, and Y.Ohkuma (2005).
Studies of Schizosaccharomyces pombe TFIIE indicate conformational and functional changes in RNA polymerase II at transcription initiation.
  Genes Cells, 10, 207-224.  
15591044 K.J.Armache, S.Mitterweger, A.Meinhart, and P.Cramer (2005).
Structures of complete RNA polymerase II and its subcomplex, Rpb4/7.
  J Biol Chem, 280, 7131-7134.
PDB codes: 1wcm 1y14
15942958 K.Shakib, J.T.Norman, L.G.Fine, L.R.Brown, and J.Godovac-Zimmermann (2005).
Proteomics profiling of nuclear proteins for kidney fibroblasts suggests hypoxia, meiosis, and cancer may meet in the nucleus.
  Proteomics, 5, 2819-2838.  
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.  
15808512 M.L.Kireeva, B.Hancock, G.H.Cremona, W.Walter, V.M.Studitsky, and M.Kashlev (2005).
Nature of the nucleosomal barrier to RNA polymerase II.
  Mol Cell, 18, 97.  
16214896 M.Palangat, D.B.Renner, D.H.Price, and R.Landick (2005).
A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS.
  Proc Natl Acad Sci U S A, 102, 15036-15041.  
15720542 S.Borukhov, J.Lee, and O.Laptenko (2005).
Bacterial transcription elongation factors: new insights into molecular mechanism of action.
  Mol Microbiol, 55, 1315-1324.  
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.  
15632064 Y.Huang, R.V.Intine, A.Mozlin, S.Hasson, and R.J.Maraia (2005).
Mutations in the RNA polymerase III subunit Rpc11p that decrease RNA 3' cleavage activity increase 3'-terminal oligo(U) length and La-dependent tRNA processing.
  Mol Cell Biol, 25, 621-636.  
15606780 A.Kulbachinskiy, A.Feklistov, I.Krasheninnikov, A.Goldfarb, and V.Nikiforov (2004).
Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB.
  Eur J Biochem, 271, 4921-4931.  
15507123 A.Nakata, T.Ito, M.Nagata, S.Hori, and K.Sekimizu (2004).
GRIP1tau, a novel PDZ domain-containing transcriptional activator, cooperates with the testis-specific transcription elongation factor SII-T1.
  Genes Cells, 9, 1125-1135.  
15294156 A.Perederina, V.Svetlov, M.N.Vassylyeva, T.H.Tahirov, S.Yokoyama, I.Artsimovitch, and D.G.Vassylyev (2004).
Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription.
  Cell, 118, 297-309.
PDB code: 1tjl
15294154 B.E.Nickels, and A.Hochschild (2004).
Regulation of RNA polymerase through the secondary channel.
  Cell, 118, 281-284.  
15003120 C.Brochier, P.Forterre, and S.Gribaldo (2004).
Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox.
  Genome Biol, 5, R17.  
15082542 F.Malagon, A.H.Tong, B.K.Shafer, and J.N.Strathern (2004).
Genetic interactions of DST1 in Saccharomyces cerevisiae suggest a role of TFIIS in the initiation-elongation transition.
  Genetics, 166, 1215-1227.  
15489286 H.Hieronymus, M.C.Yu, and P.A.Silver (2004).
Genome-wide mRNA surveillance is coupled to mRNA export.
  Genes Dev, 18, 2652-2662.  
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
15479635 H.T.Chen, and S.Hahn (2004).
Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC.
  Cell, 119, 169-180.  
15200952 J.Mukhopadhyay, E.Sineva, J.Knight, R.M.Levy, and R.H.Ebright (2004).
Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel.
  Mol Cell, 14, 739-751.  
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
15273278 M.E.Mysiak, P.E.Holthuizen, and P.C.van der Vliet (2004).
The adenovirus priming protein pTP contributes to the kinetics of initiation of DNA replication.
  Nucleic Acids Res, 32, 3913-3920.  
15359273 M.Wery, E.Shematorova, B.Van Driessche, J.Vandenhaute, P.Thuriaux, and V.Van Mullem (2004).
Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS.
  EMBO J, 23, 4232-4242.  
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.  
15165185 O.da Costa e Silva, R.Lorbiecke, P.Garg, L.Müller, M.Wassmann, P.Lauert, M.Scanlon, A.P.Hsia, P.S.Schnable, K.Krupinska, and U.Wienand (2004).
The Etched1 gene of Zea mays (L.) encodes a zinc ribbon protein that belongs to the transcriptionally active chromosome (TAC) of plastids and is similar to the transcription factor TFIIS.
  Plant J, 38, 923-939.  
15196470 P.Cramer (2004).
RNA polymerase II structure: from core to functional complexes.
  Curr Opin Genet Dev, 14, 218-226.  
15145350 R.J.Sims, S.S.Mandal, and D.Reinberg (2004).
Recent highlights of RNA-polymerase-II-mediated transcription.
  Curr Opin Cell Biol, 16, 263-271.  
15114340 S.Hahn (2004).
Structure and mechanism of the RNA polymerase II transcription machinery.
  Nat Struct Mol Biol, 11, 394-403.  
15130130 U.Lange, and W.Hausner (2004).
Transcriptional fidelity and proofreading in Archaea and implications for the mechanism of TFS-induced RNA cleavage.
  Mol Microbiol, 52, 1133-1143.  
15096519 X.Q.Gong, Y.A.Nedialkov, and Z.F.Burton (2004).
Alpha-amanitin blocks translocation by human RNA polymerase II.
  J Biol Chem, 279, 27422-27427.  
14506279 C.Zhang, H.Yan, and Z.F.Burton (2003).
Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II.
  J Biol Chem, 278, 50101-50111.  
14668436 E.Sosunova, V.Sosunov, M.Kozlov, V.Nikiforov, A.Goldfarb, and A.Mustaev (2003).
Donation of catalytic residues to RNA polymerase active center by transcription factor Gre.
  Proc Natl Acad Sci U S A, 100, 15469-15474.  
12914698 N.Opalka, M.Chlenov, P.Chacon, W.J.Rice, W.Wriggers, and S.A.Darst (2003).
Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.
  Cell, 114, 335-345.  
14633991 O.Laptenko, J.Lee, I.Lomakin, and S.Borukhov (2003).
Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase.
  EMBO J, 22, 6322-6334.  
12914690 R.C.Conaway, S.E.Kong, and J.W.Conaway (2003).
TFIIS and GreB: two like-minded transcription elongation factors with sticky fingers.
  Cell, 114, 272-274.  
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