4IWR

C.Esp1396I bound to a 25 base pair operator site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report



Literature

Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.

Martin, R.N.McGeehan, J.E.Ball, N.J.Streeter, S.D.Thresh, S.J.Kneale, G.G.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 962-966

  • DOI: 10.1107/S174430911302126X
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The controller protein of the type II restriction-modification (RM) system Esp1396I binds to three distinct DNA operator sequences upstream of the methyltransferase and endonuclease genes in order to regulate their expression. Previous biophysical an ...

    The controller protein of the type II restriction-modification (RM) system Esp1396I binds to three distinct DNA operator sequences upstream of the methyltransferase and endonuclease genes in order to regulate their expression. Previous biophysical and crystallographic studies have shown molecular details of how the controller protein binds to the operator sites with very different affinities. Here, two protein-DNA co-crystal structures containing portions of unbound DNA from native operator sites are reported. The DNA in both complexes shows significant distortion in the region between the conserved symmetric sequences, similar to that of a DNA duplex when bound by the controller protein (C-protein), indicating that the naked DNA has an intrinsic tendency to bend when not bound to the C-protein. Moreover, the width of the major groove of the DNA adjacent to a bound C-protein dimer is observed to be significantly increased, supporting the idea that this DNA distortion contributes to the substantial cooperativity found when a second C-protein dimer binds to the operator to form the tetrameric repression complex.


    Related Citations: 
    • Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.
      McGeehan, J.E., Ball, N.J., Streeter, S.D., Thresh, S.J., Kneale, G.G.
      (2012) Nucleic Acids Res 40: 4158
    • The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.
      Ball, N.J., McGeehan, J.E., Streeter, S.D., Thresh, S.J., Kneale, G.G.
      (2012) Nucleic Acids Res 40: 10532
    • Structure of the restriction-modification controller protein C.Esp1396I.
      Ball, N., Streeter, S.D., Kneale, G.G., McGeehan, J.E.
      (2009) Acta Crystallogr D Biol Crystallogr 65: 900

    Organizational Affiliation

    Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry I Street, Portsmouth, Hampshire PO1 2DY, England.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regulatory proteinA, B, E, F82Enterobacter sp. RFL1396Mutation(s): 0 
Gene Names: esp1396IC
Find proteins for Q8GGH0 (Enterobacter sp. RFL1396)
Explore Q8GGH0 
Go to UniProtKB:  Q8GGH0
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganism
DNA (25-MER)C, G25N/A

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Entity ID: 3
MoleculeChainsLengthOrganism
DNA (25-MER)D, H25N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.02α = 90
b = 48.02β = 90
c = 218.35γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-11
    Type: Initial release