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PDBsum entry 2waq
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protein ligands metals Protein-protein interface(s) links
Transcription PDB id
2waq

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
841 a.a. *
1090 a.a. *
367 a.a. *
260 a.a. *
174 a.a. *
90 a.a. *
113 a.a. *
74 a.a. *
82 a.a. *
91 a.a. *
64 a.a. *
43 a.a. *
45 a.a. *
Ligands
F3S
Metals
_MG
_ZN ×9
* Residue conservation analysis
PDB id:
2waq
Name: Transcription
Title: The complete structure of the archaeal 13-subunit DNA-directed RNA polymerase
Structure: DNA-directed RNA polymerase rpo1n subunit. Chain: a. DNA-directed RNA polymerase rpo2 subunit. Chain: b. DNA-directed RNA polymerase rpo1c subunit. Chain: c. DNA-directed RNA polymerase rpo3 subunit. Chain: d. DNA-directed RNA polymerase rpo7 subunit.
Source: Sulfolobus shibatae. Organism_taxid: 2286. Organism_taxid: 2286
Resolution:
3.35Å     R-factor:   0.274     R-free:   0.341
Authors: Y.Korkhin,U.M.Unligil,O.Littlefield,P.J.Nelson,D.I.Stuart,P.B.Sigler, S.D.Bell,N.G.A.Abrescia
Key ref: Y.Korkhin et al. (2009). Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure. Plos Biol, 7, e1000102. PubMed id: 19419240
Date:
11-Feb-09     Release date:   19-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
B8YB53  (B8YB53_SULSH) -  DNA-directed RNA polymerase subunit Rpo1N from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		 
Seq:
Struc: 		880 a.a.
841 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB55  (B8YB55_SULSH) -  DNA-directed RNA polymerase subunit Rpo2 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1128 a.a.
1090 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB54  (B8YB54_SULSH) -  DNA-directed RNA polymerase subunit Rpo1C from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		392 a.a.
367 a.a.*
Protein chain
Pfam   ArchSchema ?
B8YB56  (B8YB56_SULSH) -  DNA-directed RNA polymerase subunit Rpo3 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		265 a.a.
260 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB57  (B8YB57_SULSH) -  DNA-directed RNA polymerase subunit Rpo7 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		180 a.a.
174 a.a.*
Protein chain
Pfam   ArchSchema ?
B8YB58  (B8YB58_SULSH) -  DNA-directed RNA polymerase subunit Rpo4 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		113 a.a.
90 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB59  (B8YB59_SULSH) -  DNA-directed RNA polymerase subunit Rpo8 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		131 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB60  (B8YB60_SULSH) -  DNA-directed RNA polymerase subunit Rpo5 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		84 a.a.
74 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB61  (B8YB61_SULSH) -  DNA-directed RNA polymerase subunit Rpo6 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		95 a.a.
82 a.a.*
Protein chain
Pfam   ArchSchema ?
B8YB62  (B8YB62_SULSH) -  DNA-directed RNA polymerase subunit Rpo11 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		92 a.a.
91 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB63  (B8YB63_SULSH) -  DNA-directed RNA polymerase subunit Rpo10 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		66 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB64  (B8YB64_SULSH) -  DNA-directed RNA polymerase subunit Rpo12 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		48 a.a.
43 a.a.
Protein chain
Pfam   ArchSchema ?
B8YB65  (B8YB65_SULSH) -  DNA-directed RNA polymerase subunit Rpo13 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)
Seq:
Struc: 		104 a.a.
45 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, K, L, N, P, Q: 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    
 
 
Plos Biol 7:e1000102 (2009)
PubMed id: 19419240  
 
 
Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure.
Y.Korkhin, U.M.Unligil, O.Littlefield, P.J.Nelson, D.I.Stuart, P.B.Sigler, S.D.Bell, N.G.Abrescia.
 
  ABSTRACT  
 
The archaeal RNA polymerase (RNAP) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation. To deepen our knowledge of cellular transcription, we have determined the structure of the 13-subunit DNA-directed RNAP from Sulfolobus shibatae at 3.35 A resolution. The structure contains the full complement of subunits, including RpoG/Rpb8 and the equivalent of the clamp-head and jaw domains of the eukaryotic Rpb1. Furthermore, we have identified subunit Rpo13, an RNAP component in the order Sulfolobales, which contains a helix-turn-helix motif that interacts with the RpoH/Rpb5 and RpoA'/Rpb1 subunits. Its location and topology suggest a role in the formation of the transcription bubble.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265759 D.Grohmann, D.Klose, D.Fielden, and F.Werner (2011).
FRET (fluorescence resonance energy transfer) sheds light on transcription.
  Biochem Soc Trans, 39, 122-127.  
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
21233849 F.Werner, and D.Grohmann (2011).
Evolution of multisubunit RNA polymerases in the three domains of life.
  Nat Rev Microbiol, 9, 85-98.  
21265754 N.Peng, X.Ao, Y.X.Liang, and Q.She (2011).
Archaeal promoter architecture and mechanism of gene activation.
  Biochem Soc Trans, 39, 99.  
21250781 S.H.Jun, M.J.Reichlen, M.Tajiri, and K.S.Murakami (2011).
Archaeal RNA polymerase and transcription regulation.
  Crit Rev Biochem Mol Biol, 46, 27-40.  
20598889 A.Spang, R.Hatzenpichler, C.Brochier-Armanet, T.Rattei, P.Tischler, E.Spieck, W.Streit, D.A.Stahl, M.Wagner, and C.Schleper (2010).
Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota.
  Trends Microbiol, 18, 331-340.  
20967027 C.Fernández-Tornero, B.Böttcher, U.J.Rashid, U.Steuerwald, B.Flörchinger, D.P.Devos, D.Lindner, and C.W.Müller (2010).
Conformational flexibility of RNA polymerase III during transcriptional elongation.
  EMBO J, 29, 3762-3772.  
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.  
20363950 J.Iqbal, and S.A.Qureshi (2010).
Selective depletion of Sulfolobus solfataricus transcription factor E under heat shock conditions.
  J Bacteriol, 192, 2887-2891.  
20026480 R.Carter, and G.Drouin (2010).
The increase in the number of subunits in eukaryotic RNA polymerase III relative to RNA polymerase II is due to the permanent recruitment of general transcription factors.
  Mol Biol Evol, 27, 1035-1043.  
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.  
20833321 S.Payankaulam, L.M.Li, and D.N.Arnosti (2010).
Transcriptional repression: conserved and evolved features.
  Curr Biol, 20, R764-R771.  
19880312 A.Hirata, and K.S.Murakami (2009).
Archaeal RNA polymerase.
  Curr Opin Struct Biol, 19, 724-731.  
19492989 D.Grohmann, A.Hirtreiter, and F.Werner (2009).
RNAP subunits F/E (RPB4/7) are stably associated with archaeal RNA polymerase: using fluorescence anisotropy to monitor RNAP assembly in vitro.
  Biochem J, 421, 339-343.  
19828044 F.Blombach, K.S.Makarova, J.Marrero, B.Siebers, E.V.Koonin, and J.van der Oost (2009).
Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea.
  Biol Direct, 4, 39.  
19640276 J.P.Daniels, S.Kelly, B.Wickstead, and K.Gull (2009).
Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea.
  Biol Direct, 4, 24.  
19460096 S.Paytubi, and M.F.White (2009).
The crenarchaeal DNA damage-inducible transcription factor B paralogue TFB3 is a general activator of transcription.
  Mol Microbiol, 72, 1487-1499.  
19749050 T.J.Santangelo, L.Cubonová, K.M.Skinner, and J.N.Reeve (2009).
Archaeal intrinsic transcription termination in vivo.
  J Bacteriol, 191, 7102-7108.  
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.

 

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