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PDBsum entry 2gho

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protein Protein-protein interface(s) links
Transferase PDB id
2gho
Jmol
Contents
Protein chains
230 a.a. *
1114 a.a. *
1196 a.a. *
* Residue conservation analysis
PDB id:
2gho
Name: Transferase
Title: Recombinant thermus aquaticus RNA polymerase for structural studies
Structure: DNA-directed RNA polymerase alpha chain. Chain: a, b. Synonym: rnap alpha subunit, transcriptase alpha chain, RNA polymerase alpha subunit. Engineered: yes. DNA-directed RNA polymerase beta chain. Chain: c. Synonym: rnap beta subunit, transcriptase beta chain, RNA polymerase beta subunit.
Source: Thermus aquaticus. Organism_taxid: 271. Gene: rpoa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rpob. Gene: rpoc.
Biol. unit: Tetramer (from PQS)
Resolution:
5.00Å     R-factor:   0.336     R-free:   0.337
Authors: V.Lamour,S.A.Darst
Key ref:
K.Kuznedelov et al. (2006). Recombinant Thermus aquaticus RNA polymerase for structural studies. J Mol Biol, 359, 110-121. PubMed id: 16618493 DOI: 10.1016/j.jmb.2006.03.009
Date:
27-Mar-06     Release date:   23-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9KWU8  (RPOA_THEAQ) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
314 a.a.
230 a.a.
Protein chain
Pfam   ArchSchema ?
Q9KWU7  (RPOB_THEAQ) -  DNA-directed RNA polymerase subunit beta
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1119 a.a.
1114 a.a.
Protein chain
Pfam   ArchSchema ?
Q9KWU6  (RPOC_THEAQ) -  DNA-directed RNA polymerase subunit beta'
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1524 a.a.
1196 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: 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     DNA repair   2 terms 
  Biochemical function     transferase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2006.03.009 J Mol Biol 359:110-121 (2006)
PubMed id: 16618493  
 
 
Recombinant Thermus aquaticus RNA polymerase for structural studies.
K.Kuznedelov, V.Lamour, G.Patikoglou, M.Chlenov, S.A.Darst, K.Severinov.
 
  ABSTRACT  
 
Advances in the structural biology of bacterial transcription have come from studies of RNA polymerases (RNAPs) from the thermophilic eubacteria Thermus aquaticus (Taq) and Thermus thermophilus (Tth). These structural studies have been limited by the fact that only endogenous Taq or Tth RNAP, laboriously purified from large quantities of Taq or Tth cell paste and offering few options for genetic modification, is suitable for structural studies. Recombinant systems for the preparation of Taq RNAP by co-overexpression and assembly in the heterologous host, Escherichia coli, have been described, but these did not yield enzyme suitable for crystallographic studies. Here we describe recombinant systems for the preparation of Taq RNAP harboring full or partial deletions of the Taq beta' non-conserved domain (NCD), yielding enzyme suitable for crystallographic studies. This opens the way for structural studies of genetically manipulated enzymes, allowing the preparation of more crystallizable enzymes and facilitating detailed structure/function analysis. Characterization of the Taqbeta'NCD deletion mutants generated in this study showed that the beta'NCD is important for the efficient binding of the sigma subunit, confirming previous hypotheses. Finally, preliminary structural analysis (at 4.1Angstroms resolution) of one of the recombinant mutants revealed a previously unobserved conformation of the beta-flap, further defining the range of conformations accessible to this flexible structural element.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystallization of eTaqRNAP versus rTaqRNAP. (a) Photomicrograph of an eTaqRNAP crystal.4 (b) A 0.3° oscillation diffraction image from an eTaqRNAP crystal. The edge of the CCD plate corresponds to 3.1 Å resolution. (c) Photomicrograph of rTaqRNAP spherulites.
Figure 5.
Figure 5. rTaqRNAP-d0 crystal, diffraction, and electron density map. (a) Photomicrograph of a rTaqRNAP-d0 form II crystal (Table 2). The largest dimension of the crystal is about 0.7 mm. (b) A 0.3° oscillation diffraction image from an rTaqRNAP-d0 form II crystal. The white arrow denotes the innermost ice ring, which occurs at 3.9 Å resolution. The area within the green box is magnified in (c). (c) Magnified region of the diffraction pattern shown in (b), showing diffraction spots extending nearly to 3.9 Å resolution. (d) 2|F[o]| -|F[c]| electron density map (4.1 Å resolution) from rTaqRNAP-d0 (blue net). The a-carbon backbone of the final structural model is superimposed (b', pink; b, cyan). The b-flap-tip-helix, which is found in a unique conformation in this structure, is highlighted (*).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 110-121) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19895820 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: sequence analysis.
  J Mol Biol, 395, 671-685.  
18948199 I.Artsimovitch, and T.M.Henkin (2009).
In vitro approaches to analysis of transcription termination.
  Methods, 47, 37-43.  
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.  
18574242 N.Barinova, K.Kuznedelov, K.Severinov, and A.Kulbachinskiy (2008).
Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA.
  J Biol Chem, 283, 22482-22489.  
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.