4OB4

Structure of the S. venezulae BldD DNA-binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development.

Tschowri, N.Schumacher, M.A.Schlimpert, S.Chinnam, N.B.Findlay, K.C.Brennan, R.G.Buttner, M.J.

(2014) Cell 158: 1136-1147

  • DOI: 10.1016/j.cell.2014.07.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The cyclic dinucleotide c-di-GMP is a signaling molecule with diverse functions in cellular physiology. Here, we report that c-di-GMP can assemble into a tetramer that mediates the effective dimerization of a transcription factor, BldD, which control ...

    The cyclic dinucleotide c-di-GMP is a signaling molecule with diverse functions in cellular physiology. Here, we report that c-di-GMP can assemble into a tetramer that mediates the effective dimerization of a transcription factor, BldD, which controls the progression of multicellular differentiation in sporulating actinomycete bacteria. BldD represses expression of sporulation genes during vegetative growth in a manner that depends on c-di-GMP-mediated dimerization. Structural and biochemical analyses show that tetrameric c-di-GMP links two subunits of BldD through their C-terminal domains, which are otherwise separated by ~10 Å and thus cannot effect dimerization directly. Binding of the c-di-GMP tetramer by BldD is selective and requires a bipartite RXD-X8-RXXD signature. The findings indicate a unique mechanism of protein dimerization and the ability of nucleotide signaling molecules to assume alternative oligomeric states to effect different functions.


    Organizational Affiliation

    Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative DNA-binding protein
A, B, C
71Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)Mutation(s): 0 
Find proteins for Q7AKQ8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  Q7AKQ8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.230 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.970α = 90.00
b = 79.970β = 90.00
c = 117.400γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SCALAdata scaling
ADSCdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Structure summary