4OB4

Structure of the S. venezulae BldD DNA-binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.236 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.cell.2014.07.022
  • Primary Citation of Related Structures:  
    4OAY, 4OAZ, 4OB4, 5KHD

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative DNA-binding protein
A, B, C
71Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: bldDSAV_6861SCO1489
UniProt
Find proteins for Q7AKQ8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q7AKQ8 
Go to UniProtKB:  Q7AKQ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7AKQ8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.236 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.97α = 90
b = 79.97β = 90
c = 117.4γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Structure summary
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description