6JHE

Crystal Structure of Bacillus subtilis SigW domain 4 in complexed with -35 element DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.101 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


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Literature

Structural analysis of the recognition of the -35 promoter element by SigW from Bacillus subtilis.

Kwon, E.Devkota, S.R.Pathak, D.Dahal, P.Kim, D.Y.

(2019) Plos One 14: e0221666-e0221666

  • DOI: 10.1371/journal.pone.0221666

  • PubMed Abstract: 
  • Sigma factors are key proteins that mediate the recruitment of RNA polymerase to the promoter regions of genes, for the initiation of bacterial transcription. Multiple sigma factors in a bacterium selectively recognize their cognate promoter sequence ...

    Sigma factors are key proteins that mediate the recruitment of RNA polymerase to the promoter regions of genes, for the initiation of bacterial transcription. Multiple sigma factors in a bacterium selectively recognize their cognate promoter sequences, thereby inducing the expression of their own regulons. In this paper, we report the crystal structure of the σ4 domain of Bacillus subtilis SigW bound to the -35 promoter element. Purine-specific hydrogen bonds of the -35 promoter element with the recognition helix α9 of the σ4 domain occurs at three nucleotides of the consensus sequence (G-35, A-34, and G'-31 in G-35A-34A-33A-32C-31C-30T-29). The hydrogen bonds of the backbone with the α7 and α8 of the σ4 domain occurs at G'-30. These results elucidate the structural basis of the selective recognition of the promoter by SigW. In addition, comparison of SigW structures complexed with the -35 promoter element or with anti-sigma RsiW reveals that DNA recognition and anti-sigma factor binding of SigW are mutually exclusive.


    Organizational Affiliation

    College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ECF RNA polymerase sigma factor SigW
A
64Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: sigW (ybbL)
Find proteins for Q45585 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q45585
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*GP*AP*AP*AP*CP*CP*TP*TP*T)-3')B11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*GP*GP*TP*TP*TP*CP*AP*A)-3')C11synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.101 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.247 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.620α = 90.00
b = 61.620β = 90.00
c = 119.971γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release