3G5G

Crystal Structure of the Wild-Type Restriction-Modification Controller Protein C.Esp1396I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 900-905

  • DOI: 10.1107/S0907444909020514
  • Primary Citation of Related Structures:  3FYA
  • Also Cited By: 4F8D, 4FN3, 4I6R, 4I6T, 4I6U, 4I8T, 4IA8, 4IVZ, 4IWR

  • PubMed Abstract: 
  • The controller protein of the Esp1396I restriction-modification (R-M) system binds differentially to three distinct operator sequences upstream of the methyltransferase (M) and endonuclease (R) genes to regulate the timing of gene expression. The cry ...

    The controller protein of the Esp1396I restriction-modification (R-M) system binds differentially to three distinct operator sequences upstream of the methyltransferase (M) and endonuclease (R) genes to regulate the timing of gene expression. The crystal structure of a complex of the protein with two adjacent operator DNA sequences has been reported; however, the structure of the free protein has not yet been determined. Here, the crystal structure of the free protein is reported, with seven dimers in the asymmetric unit. Two of the 14 monomers show an alternative conformation to the major conformer in which the side chains of residues 43-46 in the loop region flanking the DNA-recognition helix are displaced by up to 10 A. It is proposed that the adoption of these two conformational states may play a role in DNA-sequence promiscuity. The two alternative conformations are also found in the R35A mutant structure, which is otherwise identical to the native protein. Comparison of the free and bound protein structures shows a 1.4 A displacement of the recognition helices when the dimer is bound to its DNA target.


    Related Citations: 
    • Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.
      McGeehan, J.E.,Streeter, S.D.,Thresh, S.J.,Ball, N.,Ravelli, R.B.,Kneale, G.G.
      (2008) NUCLEIC ACIDS RES. 36: 4778


    Organizational Affiliation

    Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regulatory protein
A, B, C, D, E, F, G, H, I, J, K, L, M, N
99Enterobacter sp. RFL1396Gene Names: esp1396IC
Find proteins for Q8GGH0 (Enterobacter sp. RFL1396)
Go to UniProtKB:  Q8GGH0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.237 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 128.717α = 90.00
b = 128.717β = 90.00
c = 137.508γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
MxCuBEdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2012-03-28
    Type: Database references