6IDO

Crystal structure of Klebsiella pneumoniae sigma4 of sigmaS fusing with the RNA polymerase beta-flap-tip-helix in complex with -35 element DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for -35 element recognition by sigma4chimera proteins and their interactions with PmrA response regulator.

Lou, Y.C.Chou, C.C.Yeh, H.H.Chien, C.Y.Sadotra, S.Hsu, C.H.Chen, C.

(2020) Proteins 88: 69-81

  • DOI: 10.1002/prot.25768
  • Primary Citation of Related Structures:  
    6IDO

  • PubMed Abstract: 
  • In class II transcription activation, the transcription factor normally binds to the promoter near the -35 position and contacts the domain 4 of σ factors (σ 4 ) to activate transcription. However, σ 4 of σ 70 appe ...

    In class II transcription activation, the transcription factor normally binds to the promoter near the -35 position and contacts the domain 4 of σ factors (σ 4 ) to activate transcription. However, σ 4 of σ 70 appears to be poorly folded on its own. Here, by fusing σ 4 with the RNA polymerase β-flap-tip-helix, we constructed two σ 4 chimera proteins, one from σ 70 σ 4 70 c and another from σ S σ 4 S c of Klebsiella pneumoniae. The two chimera proteins well folded into a monomeric form with strong binding affinities for -35 element DNA. Determining the crystal structure of σ 4 S c in complex with -35 element DNA revealed that σ 4 S c adopts a similar structure as σ 4 in the Escherichia coli RNA polymerase σ S holoenzyme and recognizes -35 element DNA specifically by several conserved residues from the helix-turn-helix motif. By using nuclear magnetic resonance (NMR), σ 4 70 c was demonstrated to recognize -35 element DNA similar to σ 4 S c . Carr-Purcell-Meiboom-Gill relaxation dispersion analyses showed that the N-terminal helix and the β-flap-tip-helix of σ 4 70 c have a concurrent transient α-helical structure and DNA binding reduced the slow dynamics on σ 4 70 c . Finally, only σ 4 70 c was shown to interact with the response regulator PmrA and its promoter DNA. The chimera proteins are capable of -35 element DNA recognition and can be used for study with transcription factors or other factors that interact with domain 4 of σ factors.


    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helixAB115Escherichia coliKlebsiella pneumoniae
This entity is chimeric
Mutation(s): 1 
Gene Names: rpoS
EC: 2.7.7.6
Find proteins for A6TGP0 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TGP0 
Go to UniProtKB:  A6TGP0
Find proteins for P13445 (Escherichia coli (strain K12))
Explore P13445 
Go to UniProtKB:  P13445
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3')C, E15Klebsiella pneumoniae
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3')D, F16Klebsiella pneumoniae
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.75 Å
      • R-Value Free: 0.253 
      • R-Value Work: 0.223 
      • R-Value Observed: 0.226 
      • Space Group: I 4 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 154.54α = 90
      b = 154.54β = 90
      c = 144.96γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data scaling
      PHASERphasing
      Cootmodel building
      HKL-2000data reduction

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2019-09-11
        Type: Initial release
      • Version 1.1: 2020-03-25
        Changes: Database references