spacer
spacer

PDBsum entry 2vum
Go to PDB code: 
protein dna_rna ligands metals Protein-protein interface(s) links
Transferase PDB id
2vum

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
1418 a.a. *
1106 a.a. *
266 a.a. *
177 a.a. *
214 a.a. *
84 a.a. *
171 a.a. *
133 a.a. *
119 a.a. *
65 a.a. *
114 a.a. *
46 a.a. *
DNA/RNA
Ligands
ASN-HYP-ILX-TRX-
GLY-ILE-GLY-CSX
Metals
_MG
_ZN ×8
* Residue conservation analysis
PDB id:
2vum
Name: Transferase
Title: Alpha-amanitin inhibited complete RNA polymerase ii elongation complex
Structure: DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: RNA polymerase ii subunit b1, RNA polymerase ii subunit 1, DNA-directed RNA polymerase iii largest subunit, b220, DNA-directed RNA polymerase ii largest subunit. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: DNA-directed RNA polymerase ii 140 kda, RNA polymerase ii subunit 2, DNA-directed RNA polymerase ii 140 kda polypeptide, b150
Source: Saccharomyces cerevisiae. Bakers' yeast. Organism_taxid: 4932. Amanita phalloides. Death cap. Organism_taxid: 67723. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.
Resolution:
3.40Å     R-factor:   0.255     R-free:   0.288
Authors: F.Brueckner,P.Cramer
Key ref:
F.Brueckner and P.Cramer (2008). Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat Struct Biol, 15, 811-818. PubMed id: 18552824 DOI: 10.1038/nsmb.1458
Date:
27-May-08     Release date:   17-Jun-08    
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.
1418 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.
1106 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 ?
P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		221 a.a.
177 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.
214 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.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		171 a.a.
171 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-A-C-T-A-C-T-T-G-A-G-C-T 13 bases
  A-A-G-A-C-C-A-G-G-C 10 bases
  A-G-C-T-C-A-A-G-T-A-G-T-T-A-C-G-C-C-BRU-G-G-T-C-A-T 25 bases

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K: 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: 10.1038/nsmb.1458 Nat Struct Biol 15:811-818 (2008)
PubMed id: 18552824  
 
 
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.
F.Brueckner, P.Cramer.
 
  ABSTRACT  
 
To study how RNA polymerase II translocates after nucleotide incorporation, we prepared elongation complex crystals in which pre- and post-translocation states interconvert. Crystal soaking with the inhibitor alpha-amanitin locked the elongation complex in a new state, which was refined at 3.4-A resolution and identified as a possible translocation intermediate. The DNA base entering the active site occupies a 'pretemplating' position above the central bridge helix, which is shifted and occludes the templating position. A leucine residue in the trigger loop forms a wedge at the shifted bridge helix, but moves by 13 A to close the active site during nucleotide incorporation. Our results support a Brownian ratchet mechanism that involves swinging of the trigger loop between open, wedged and closed positions, and suggest that alpha-amanitin impairs nucleotide incorporation and translocation by trapping the trigger loop and bridge helix.
 
  Selected figure(s)  
 
Figure 4.
(a,b) Superposition of the trigger loops and bridge helices in the -amanitin inhibited Pol II EC and the free T. thermophilus (Tth) RNA polymerase^6. The trigger loop residue Leu1081 (S. cerevisiae (Sc) Pol II) or its homologous residue Met1238 (Tth) forms a wedge between the bridge helix and helix 37 in Pol II or G' in Tth. The views are from the top (a) or the side (b), as in Figure 3b or 1e, respectively. In the -amanitin–inhibited Pol II EC, the central bridge helix is shifted, whereas in the bacterial holoenzyme it adopts a flipped-out conformation. (c,d) Four possible states of the EC. Above to below, the pretranslocation state (PDB 1I6H)^1, a potential transition state with a modeled flipped-out bridge helix (PDB 1IW7)^17, the -amanitin–inhibited EC (the apparent translocation intermediate with the shifted bridge helix, this study), and the post-translocation state (PDB 1Y1W)^2 are shown with space-filling models (c) or ribbon diagrams (d). The bridge helix residues Ala832/Ala1089 (Pol II/Tth) and Thr831/Thr1088 (Pol II/Tth) are highlighted in yellow and brown, respectively. (e,f) Comparison of trigger loop conformations. Pol II EC structures in the post-translocation state (PDB 1Y1W)^2, with bound NTP substrate (PDB 2E2H)^4, and in the intermediary state are superimposed. Nucleic acids and metal A are from the translocation intermediate. The trigger loops of the three structures are depicted in dark red (wedged, translocation intermediate), light blue (open, 1Y1W) and yellow (closed, 2E2H, labels in black). (f) Also depicted are the bridge helix (green, apparent translocation intermediate) and the NTP in the insertion site (orange, 2E2H). (g) Comparison of bridge helix conformations in the -amanitin–inhibited EC (green, with residues Ala832 and Thr831 highlighted in yellow and brown, respectively), the post-translocation EC^2 (light green) and the core Pol II EC with bound NTP^4 (beige). 		Figure 5.
Schematic representation of the extended model for the NAC. The vertical dashed line indicates register +1. For details, refer to text.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2008, 15, 811-818) copyright 2008.  
  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
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.  
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.  
20482321 P.Cramer (2010).
Towards molecular systems biology of gene transcription and regulation.
  Biol Chem, 391, 731-735.  
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.  
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.  
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.  
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.  
18946472 G.A.Belogurov, M.N.Vassylyeva, A.Sevostyanova, J.R.Appleman, A.X.Xiang, R.Lira, S.E.Webber, S.Klyuyev, E.Nudler, I.Artsimovitch, and D.G.Vassylyev (2009).
Transcription inactivation through local refolding of the RNA polymerase structure.
  Nature, 457, 332-335.
PDB code: 3eql
19758983 G.E.Damsma, and P.Cramer (2009).
Molecular basis of transcriptional mutagenesis at 8-oxoguanine.
  J Biol Chem, 284, 31658-31663.
PDB codes: 3i4m 3i4n
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.  
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.  
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
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.  
18957193 R.Sousa (2008).
Tie me up, tie me down: inhibiting RNA polymerase.
  Cell, 135, 205-207.  
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.

 

spacer
spacer