3ZPL

Crystal structure of Sco3205, a MarR family transcriptional regulator from Streptomyces coelicolor, in complex with DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

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This is version 1.2 of the entry. See complete history. 


Literature

Investigation of DNA Sequence Recognition by a Streptomycete Marr Family Transcriptional Regulator Through Surface Plasmon Resonance and X-Ray Crystallography.

Stevenson, C.E.M., Assaad, A., Chandra, G., Le, T.B.K., Greive, S.J., Bibb, M.J., Lawson, D.M.

(2013) Nucleic Acids Res 41: 7009

  • DOI: 10.1093/nar/gkt523
  • Primary Citation of Related Structures:  
    3ZPL

  • PubMed Abstract: 

    • Consistent with their complex lifestyles and rich secondary metabolite profiles, the genomes of streptomycetes encode a plethora of transcription factors, the vast majority of which are uncharacterized. Herein, we use Surface Plasmon Resonance (SPR) to identify and delineate putative operator sites for SCO3205, a MarR family transcriptional regulator from Streptomyces coelicolor that is well represented in sequenced actinomycete genomes ...

    Consistent with their complex lifestyles and rich secondary metabolite profiles, the genomes of streptomycetes encode a plethora of transcription factors, the vast majority of which are uncharacterized. Herein, we use Surface Plasmon Resonance (SPR) to identify and delineate putative operator sites for SCO3205, a MarR family transcriptional regulator from Streptomyces coelicolor that is well represented in sequenced actinomycete genomes. In particular, we use a novel SPR footprinting approach that exploits indirect ligand capture to vastly extend the lifetime of a standard streptavidin SPR chip. We define two operator sites upstream of sco3205 and a pseudopalindromic consensus sequence derived from these enables further potential operator sites to be identified in the S. coelicolor genome. We evaluate each of these through SPR and test the importance of the conserved bases within the consensus sequence. Informed by these results, we determine the crystal structure of a SCO3205-DNA complex at 2.8 Å resolution, enabling molecular level rationalization of the SPR data. Taken together, our observations support a DNA recognition mechanism involving both direct and indirect sequence readout.

    Organizational Affiliation: 

    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE MARR-FAMILY TRANSCRIPTIONAL REPRESSORA, B, E, F177Streptomyces coelicolorMutation(s): 0 
UniProt
Find proteins for Q9KYU1 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9KYU1 
Go to UniProtKB:  Q9KYU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KYU1
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*AP*AP*AP*GP*AP*TP*TP*GP*AP*GP*AP*TP*CP*TP *CP*AP*AP*TP*CP*TP*TP*DT)-3'C, D, G, H22synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.8α = 90
b = 70.8β = 90
c = 557.48γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Database references
  • Version 1.2: 2019-02-20
    Changes: Data collection, Other, Source and taxonomy