4JCY

Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OR operator complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression.

Shevtsov, M.B.Streeter, S.D.Thresh, S.J.Swiderska, A.McGeehan, J.E.Kneale, G.G.

(2015) Acta Crystallogr.,Sect.D 71: 398-407

  • DOI: 10.1107/S139900471402690X
  • Primary Citation of Related Structures:  4JCX, 4JQD

  • PubMed Abstract: 
  • In a wide variety of bacterial restriction-modification systems, a regulatory `controller' protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have ...

    In a wide variety of bacterial restriction-modification systems, a regulatory `controller' protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have recently turned our attention to a new class of controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (∼60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Csp231I C protein
A, B
98Citrobacter sp. RFL231N/A
Find proteins for Q32WH4 (Citrobacter sp. RFL231)
Go to UniProtKB:  Q32WH4
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*CP*TP*AP*AP*GP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*CP*AP*A)-3')C21N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*GP*CP*TP*AP*AP*GP*AP*TP*TP*TP*TP*CP*TP*TP*AP*GP*TP*TP*T)-3')D21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.147 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.340α = 90.00
b = 62.340β = 90.00
c = 158.080γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
DNAdata collection
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references
  • Version 1.2: 2015-04-15
    Type: Database references