PDBsum entry 2r92

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protein dna_rna metals Protein-protein interface(s) links
Transferase/RNA PDB id
Protein chains
1422 a.a. *
1112 a.a. *
267 a.a. *
178 a.a. *
214 a.a. *
88 a.a. *
171 a.a. *
135 a.a. *
116 a.a. *
65 a.a. *
112 a.a. *
46 a.a. *
_ZN ×8
* Residue conservation analysis
PDB id:
Name: Transferase/RNA
Title: Elongation complex of RNA polymerase ii with artificial rdrp scaffold
Structure: RNA (5'- r( Up Gp Cp Ap Up Ap Ap Ap Gp Ap Cp Cp Ap Gp Gp C)-3'). Chain: p. Engineered: yes. RNA (5'- r( Cp Up Up Gp Ap Cp Gp Cp Cp Up Gp Gp Up Cp Ap Ap A)-3'). Chain: t. Engineered: yes. DNA-directed RNA polymerase ii subunit rpb1.
Source: Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932
3.80Å     R-factor:   0.212     R-free:   0.246
Authors: E.Lehmann,F.Brueckner,P.Cramer
Key ref:
E.Lehmann et al. (2007). Molecular basis of RNA-dependent RNA polymerase II activity. Nature, 450, 445-449. PubMed id: 18004386 DOI: 10.1038/nature06290
12-Sep-07     Release date:   27-Nov-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1
1733 a.a.
1422 a.a.
Protein chain
Pfam   ArchSchema ?
P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2
1224 a.a.
1112 a.a.
Protein chain
Pfam   ArchSchema ?
P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3
318 a.a.
267 a.a.
Protein chain
Pfam   ArchSchema ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4
221 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1
215 a.a.
214 a.a.
Protein chain
Pfam   ArchSchema ?
P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2
155 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7
171 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3
146 a.a.
135 a.a.
Protein chain
Pfam   ArchSchema ?
P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9
122 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5
70 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11
120 a.a.
112 a.a.
Protein chain
Pfam   ArchSchema ?
P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4
70 a.a.
46 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - 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   22 terms 
  Biochemical function     RNA polymerase II activity     19 terms  


DOI no: 10.1038/nature06290 Nature 450:445-449 (2007)
PubMed id: 18004386  
Molecular basis of RNA-dependent RNA polymerase II activity.
E.Lehmann, F.Brueckner, P.Cramer.
RNA polymerase (Pol) II catalyses DNA-dependent RNA synthesis during gene transcription. There is, however, evidence that Pol II also possesses RNA-dependent RNA polymerase (RdRP) activity. Pol II can use a homopolymeric RNA template, can extend RNA by several nucleotides in the absence of DNA, and has been implicated in the replication of the RNA genomes of hepatitis delta virus (HDV) and plant viroids. Here we show the intrinsic RdRP activity of Pol II with only pure polymerase, an RNA template-product scaffold and nucleoside triphosphates (NTPs). Crystallography reveals the template-product duplex in the site occupied by the DNA-RNA hybrid during transcription. RdRP activity resides at the active site used during transcription, but it is slower and less processive than DNA-dependent activity. RdRP activity is also obtained with part of the HDV antigenome. The complex of transcription factor IIS (TFIIS) with Pol II can cleave one HDV strand, create a reactive stem-loop in the hybrid site, and extend the new RNA 3' end. Short RNA stem-loops with a 5' extension suffice for activity, but their growth to a critical length apparently impairs processivity. The RdRP activity of Pol II provides a missing link in molecular evolution, because it suggests that Pol II evolved from an ancient replicase that duplicated RNA genomes.
  Selected figure(s)  
Figure 2.
Figure 2: Crystal structure of a Pol II–RdRP complex. a, Ribbon model of Pol II (grey) with an initial, unbiased difference Fourier electron-density map (cyan, contoured at 2.2 ). The map was calculated from protein model phases. It reveals the RNA template–product duplex of scaffold RdRP-ss6 (Supplementary Fig. 2) in the active-centre cleft of Pol II. The bridge helix is in green. The catalytic metal ion A is depicted as a magenta sphere, and Zn^2+ ions as cyan spheres. The view is related to that in Fig. 1a by a 90° rotation around a vertical axis. b, Comparison of the RNA template–product duplex in the RdRP EC with the DNA–RNA hybrid duplex in the transcription EC^7. Protein structures were superimposed by fitting the active-site aspartate loops.
Figure 4.
Figure 4: Mechanism of HDV replication initiation. a, HDV-derived terminal stem-loops consisting of 5 or 6 bp enable templated incorporation of the next nucleotide(s). b, Pure Pol II–TFIIS complex cleaves the HDV antigenome terminal segment and elongates the newly formed 3' end on the addition of NTP. For cleavage, Pol II–scaffold complex (625 nM) was incubated with TFIIS (1.25 M) in transcription buffer for 60 min at 28 °C. For elongation of the cleavage product, the reaction mixture was incubated with 1 mM NTPs at 28 °C for 20 min. For lane 5, the cleavage reaction was stopped after 60 min ('Stop'). c, Difference electron density omit map for the 6-bp HDV stem-loop bound to the hybrid site of Pol II (calculated with protein phases only, contoured at 3.0 ). The disordered loop is indicated with a dashed line. The view is as in Fig. 2a. d, Superposition of the RNA template–product duplex in the HDV EC and the RdRP EC (Fig. 2) on the DNA–RNA hybrid duplex in the transcription EC^7. Protein structures were superimposed by fitting the active-site aspartate loops. e, Model of initial interaction of the HDV antigenome terminal segment with the Pol II–TFIIS complex. The stem-loop is placed in accordance with the crystal structure (c, d) and the downstream duplex in accordance with the location of the FC* RNA 3' stem. We predict that the HDV bulge passes the bridge helix and active site, where cleavage occurs.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 450, 445-449) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21415862 E.Logette, S.Schuepbach-Mallepell, M.J.Eckert, X.H.Leo, B.Jaccard, C.Manzl, A.Tardivel, A.Villunger, M.Quadroni, O.Gaide, and J.Tschopp (2011).
PIDD orchestrates translesion DNA synthesis in response to UV irradiation.
  Cell Death Differ, 18, 1036-1045.  
21233849 F.Werner, and D.Grohmann (2011).
Evolution of multisubunit RNA polymerases in the three domains of life.
  Nat Rev Microbiol, 9, 85-98.  
21396820 J.M.Maniar, and A.Z.Fire (2011).
EGO-1, a C. elegans RdRP, modulates gene expression via production of mRNA-templated short antisense RNAs.
  Curr Biol, 21, 449-459.  
21294682 Y.Maida, and K.Masutomi (2011).
RNA-dependent RNA polymerases in RNA silencing.
  Biol Chem, 392, 299-304.  
20204073 C.R.Huang, and S.J.Lo (2010).
Evolution and diversity of the human hepatitis d virus genome.
  Adv Bioinformatics, (), 323654.  
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.  
21203452 H.Pelczar, A.Woisard, J.M.Lemaître, M.Chachou, and Y.Andéol (2010).
Evidence for an RNA polymerization activity in axolotl and Xenopus egg extracts.
  PLoS One, 5, e14411.  
20634311 J.Mellor (2010).
Transcription: from regulatory ncRNA to incongruent redundancy.
  Genes Dev, 24, 1449-1455.  
20210550 J.Taylor, and M.Pelchat (2010).
Origin of hepatitis delta virus.
  Future Microbiol, 5, 393-402.  
20671709 P.Kapranov, F.Ozsolak, S.W.Kim, S.Foissac, D.Lipson, C.Hart, S.Roels, C.Borel, S.E.Antonarakis, A.P.Monaghan, B.John, and P.M.Milos (2010).
New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism.
  Nature, 466, 642-646.  
20169186 P.Parameswaran, E.Sklan, C.Wilkins, T.Burgon, M.A.Samuel, R.Lu, K.M.Ansel, V.Heissmeyer, S.Einav, W.Jackson, T.Doukas, S.Paranjape, C.Polacek, F.B.dos Santos, R.Jalili, F.Babrzadeh, B.Gharizadeh, D.Grimm, M.Kay, S.Koike, P.Sarnow, M.Ronaghi, S.W.Ding, E.Harris, M.Chow, M.S.Diamond, K.Kirkegaard, J.S.Glenn, and A.Z.Fire (2010).
Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems.
  PLoS Pathog, 6, e1000764.  
19923176 S.Y.Hong, and P.J.Chen (2010).
Phosphorylation of serine 177 of the small hepatitis delta antigen regulates viral antigenomic RNA replication by interacting with the processive RNA polymerase II.
  J Virol, 84, 1430-1438.  
19400635 B.Ding (2009).
The biology of viroid-host interactions.
  Annu Rev Phytopathol, 47, 105-131.  
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.  
19119310 J.R.Haag, O.Pontes, and C.S.Pikaard (2009).
Metal A and metal B sites of nuclear RNA polymerases Pol IV and Pol V are required for siRNA-dependent DNA methylation and gene silencing.
  PLoS ONE, 4, e4110.  
19644447 J.V.Hartig, S.Esslinger, R.Böttcher, K.Saito, and K.Förstemann (2009).
Endo-siRNAs depend on a new isoform of loquacious and target artificially introduced, high-copy sequences.
  EMBO J, 28, 2932-2944.  
19078964 L.Daxinger, T.Kanno, E.Bucher, J.van der Winden, U.Naumann, A.J.Matzke, and M.Matzke (2009).
A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation.
  EMBO J, 28, 48-57.  
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
18653455 C.H.Tseng, K.S.Jeng, and M.M.Lai (2008).
Transcription of subgenomic mRNA of hepatitis delta virus requires a modified hepatitis delta antigen that is distinct from antigenomic RNA synthesis.
  J Virol, 82, 9409-9416.  
18514566 C.S.Pikaard, J.R.Haag, T.Ream, and A.T.Wierzbicki (2008).
Roles of RNA polymerase IV in gene silencing.
  Trends Plant Sci, 13, 390-397.  
18552826 D.Haussecker, D.Cao, Y.Huang, P.Parameswaran, A.Z.Fire, and M.A.Kay (2008).
Capped small RNAs and MOV10 in human hepatitis delta virus replication.
  Nat Struct Mol Biol, 15, 714-721.  
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.  
18313387 P.D.Mariner, R.D.Walters, C.A.Espinoza, L.F.Drullinger, S.D.Wagner, J.F.Kugel, and J.A.Goodrich (2008).
Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock.
  Mol Cell, 29, 499-509.  
18632853 Y.S.Chen, W.H.Huang, S.Y.Hong, Y.G.Tsay, and P.J.Chen (2008).
ERK1/2-mediated phosphorylation of small hepatitis delta antigen at serine 177 enhances hepatitis delta virus antigenomic RNA replication.
  J Virol, 82, 9345-9358.  
18059450 I.Artsimovitch, and D.G.Vassylyev (2007).
Merging the RNA and DNA worlds.
  Nat Struct Mol Biol, 14, 1122-1123.  
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.