4IWR

C.Esp1396I bound to a 25 base pair operator site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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 69: 962-966

  • DOI: 10.1107/S174430911302126X
  • Primary Citation of Related Structures:  4I8T

  • 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: 
    • Structure of the restriction-modification controller protein C.Esp1396I.
      Ball, N.,Streeter, S.D.,Kneale, G.G.,McGeehan, J.E.
      (2009) Acta Crystallogr.,Sect.D 65: 900
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regulatory protein
A, B, E, F
82Enterobacter sp. RFL1396Gene Names: esp1396IC
Find proteins for Q8GGH0 (Enterobacter sp. RFL1396)
Go to UniProtKB:  Q8GGH0
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (25-MER)C,G25N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (25-MER)D,H25N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 48.020α = 90.00
b = 48.020β = 90.00
c = 218.350γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
DNAdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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