5VXN

Structure of two RcsB dimers bound to two parallel DNAs.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.38 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB.

Filippova, E.V.Zemaitaitis, B.Aung, T.Wolfe, A.J.Anderson, W.F.

(2018) mBio 9

  • DOI: 10.1128/mBio.01993-17
  • Primary Citation of Related Structures:  
    5W43, 5VXN

  • PubMed Abstract: 
  • RcsB is a highly conserved transcription regulator of the Rcs phosphorelay system, a complex two-component signal transduction system (N. Majdalani and S. Gottesman, Annu Rev Microbiol 59:379-405, 2005; A. J. Wolfe, Curr Opin Microbiol 13:204-209, 20 ...

    RcsB is a highly conserved transcription regulator of the Rcs phosphorelay system, a complex two-component signal transduction system (N. Majdalani and S. Gottesman, Annu Rev Microbiol 59:379-405, 2005; A. J. Wolfe, Curr Opin Microbiol 13:204-209, 2010, https://doi.org/10.1016/j.mib.2010.01.002; D. J. Clarke, Future Microbiol 5:1173-1184, 2010, https://doi.org/10.2217/fmb.10.83). RcsB plays an important role in virulence and pathogenicity in human hosts by regulating biofilm formation. RcsB can regulate transcription alone or together with its auxiliary transcription regulators by forming heterodimers. This complexity allows RcsB to regulate transcription of more than 600 bacterial genes in response to different stresses (D. Wang et al., Mol Plant Microbe Interact 25:6-17, 2012, https://doi.org/10.1094/MPMI-08-11-0207). Despite increasing knowledge of RcsB importance, molecular mechanisms that drive the ability of RcsB to control transcription of a large number of genes remain unclear. Here, we present crystal structures of unphosphorylated RcsB in complex with the consensus DNA-binding sequence of 22-mer (DNA22) and 18-mer (DNA18) of the flhDC operon from Escherichia coli determined at 3.15- and 3.37-Å resolution, respectively. The results of our structural analysis combined with the results of in vitro binding assays provide valuable insights to the protein regulatory mechanism, demonstrate how RcsB recognizes target DNA sequences, and reveal a unique oligomeric state that allows RcsB to form homo- and heterodimers. This information will help us understand the complex mechanisms of transcriptional regulation by RcsB in bacteria. IMPORTANCE RcsB is a well-studied two-component response regulator of the Rcs phosphorelay system, conserved within the family Enterobacteriaceae , which includes many pathogens. It is a global regulator, controlling more than 5% of bacterial genes associated with capsule biosynthesis, flagellar biogenesis, cell wall biosynthesis, antibiotic resistance, biofilm formation, and virulence in pathogens. Knowledge of RcsB structure represents a unique opportunity to explore mechanisms that regulate the Rcs phosphorelay system and its role in the family Enterobacteriaceae .


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulatory protein RcsBABCD216Escherichia coli K-12Mutation(s): 0 
Gene Names: rcsBb2217JW2205
Find proteins for P0DMC7 (Escherichia coli (strain K12))
Explore P0DMC7 
Go to UniProtKB:  P0DMC7
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*A)-3')E, G18Escherichia coli
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*AP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*AP*TP*A)-3')F, H18Escherichia coli
      Experimental Data & Validation

      Experimental Data

      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 74.116α = 90
      b = 113.231β = 115.37
      c = 76.868γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata processing
      XDSdata scaling
      PHASERphasing
      BLU-MAXdata collection
      Cootmodel building

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

      Revision History 

      • Version 1.0: 2018-03-07
        Type: Initial release
      • Version 1.1: 2018-03-14
        Changes: Database references
      • Version 1.2: 2019-12-11
        Changes: Author supporting evidence