3ZQL

DNA-bound form of TetR-like repressor SimR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Crystal Structure of the Tetr Family Transcriptional Repressor Simr Bound to DNA and the Role of a Flexible N-Terminal Extension in Minor Groove Binding.

Le, T.B.K.Schumacher, M.A.Lawson, D.M.Brennan, R.G.Buttner, M.J.

(2011) Nucleic Acids Res 39: 9433

  • DOI: https://doi.org/10.1093/nar/gkr640
  • Primary Citation of Related Structures:  
    3ZQL

  • PubMed Abstract: 

    SimR, a TetR-family transcriptional regulator (TFR), controls the export of simocyclinone, a potent DNA gyrase inhibitor made by Streptomyces antibioticus. Simocyclinone is exported by a specific efflux pump, SimX and the transcription of simX is repressed by SimR, which binds to two operators in the simR-simX intergenic region. The DNA-binding domain of SimR has a classical helix-turn-helix motif, but it also carries an arginine-rich N-terminal extension. Previous structural studies showed that the N-terminal extension is disordered in the absence of DNA. Here, we show that the N-terminal extension is sensitive to protease cleavage, but becomes protease resistant upon binding DNA. We demonstrate by deletion analysis that the extension contributes to DNA binding, and describe the crystal structure of SimR bound to its operator sequence, revealing that the N-terminal extension binds in the minor groove. In addition, SimR makes a number of sequence-specific contacts to the major groove via its helix-turn-helix motif. Bioinformatic analysis shows that an N-terminal extension rich in positively charged residues is a feature of the majority of TFRs. Comparison of the SimR-DNA and SimR-simocyclinone complexes reveals that the conformational changes associated with ligand-mediated derepression result primarily from rigid-body rotation of the subunits about the dimer interface.


  • Organizational Affiliation

    Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. tung.le@jic.ac.uk


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE REPRESSOR SIMREG2
A, B, C, D
267Streptomyces antibioticusMutation(s): 0 
UniProt
Find proteins for Q9AMH9 (Streptomyces antibioticus)
Explore Q9AMH9 
Go to UniProtKB:  Q9AMH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AMH9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*CP*CP*GP*TP*AP*DCP *GP*AP*A)-3'
E, G
17Streptomyces antibioticus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*GP*CP*GP*TP*AP*DCP *GP*AP*A)-3'
F, H
17Streptomyces antibioticus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.788α = 90
b = 112.613β = 90
c = 163.725γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description