3CLC

Crystal Structure of the Restriction-Modification Controller Protein C.Esp1396I Tetramer in Complex with its Natural 35 Base-Pair Operator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 4778-4787

  • DOI: 10.1093/nar/gkn448
  • Also Cited By: 4X4I, 4X4H, 4X4G, 4X4F, 4X4E, 4X4D, 4X4C, 4X4B, 4IVZ, 4FBI, 4F8D, 3G5G, 3FYA

  • PubMed Abstract: 
  • Controller (C) proteins regulate the timing of the expression of restriction and modification (R-M) genes through a combination of positive and negative feedback circuits. A single dimer bound to the operator switches on transcription of the C-gene a ...

    Controller (C) proteins regulate the timing of the expression of restriction and modification (R-M) genes through a combination of positive and negative feedback circuits. A single dimer bound to the operator switches on transcription of the C-gene and the endonuclease gene; at higher concentrations, a second dimer bound adjacently switches off these genes. Here we report the first structure of a C protein-DNA operator complex, consisting of two C protein dimers bound to the native 35 bp operator sequence of the R-M system Esp1396I. The structure reveals a role for both direct and indirect DNA sequence recognition. The structure of the DNA in the complex is highly distorted, with severe compression of the minor groove resulting in a 50 degrees bend within each operator site, together with a large expansion of the major groove in the centre of the DNA sequence. Cooperative binding between dimers governs the concentration-dependent activation-repression switch and arises, in part, from the interaction of Glu25 and Arg35 side chains at the dimer-dimer interface. Competition between Arg35 and an equivalent residue of the sigma(70) subunit of RNA polymerase for the Glu25 site underpins the switch from activation to repression of the endonuclease gene.


    Organizational Affiliation

    Biophysics Laboratories, School of Biological Sciences, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regulatory protein
A, B, C, D
82Enterobacter sp. RFL1396Mutation(s): 0 
Gene Names: esp1396IC
Find proteins for Q8GGH0 (Enterobacter sp. RFL1396)
Go to UniProtKB:  Q8GGH0
Entity ID: 2
MoleculeChainsLengthOrganism
35-MERE35N/A
Entity ID: 3
MoleculeChainsLengthOrganism
35-MERF35N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 104.480α = 90.00
b = 104.480β = 90.00
c = 139.290γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance