4JCY

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

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This is version 1.3 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 D Biol Crystallogr 71: 398-407

  • DOI: https://doi.org/10.1107/S139900471402690X
  • Primary Citation of Related Structures:  
    4JCX, 4JCY, 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 recently turned our attention to a new class of controller proteins (exemplified by C ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Csp231I C protein
A, B
98Citrobacter sp. RFL231Mutation(s): 0 
UniProt
Find proteins for Q32WH4 (Citrobacter sp. RFL231)
Explore Q32WH4 
Go to UniProtKB:  Q32WH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ32WH4
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
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')21N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
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')21N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.34α = 90
b = 62.34β = 90
c = 158.08γ = 120
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description