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 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoS,RNA polymerase beta-flap-tip-helixA,
D [auth B]
115Escherichia coliKlebsiella pneumoniae
This entity is chimeric
Mutation(s): 1 
Gene Names: rpoS
EC: 2.7.7.6
UniProt
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA6TGP0P13445
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*TP*TP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*C)-3')B [auth C],
E
15Klebsiella pneumoniae
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*AP*AP*TP*CP*G)-3')C [auth D],
F
16Klebsiella pneumoniae
Sequence Annotations
Expand
  • Reference Sequence
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  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description