1FOK

STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the multimodular endonuclease FokI bound to DNA.

Wah, D.A.Hirsch, J.A.Dorner, L.F.Schildkraut, I.Aggarwal, A.K.

(1997) Nature 388: 97-100

  • DOI: 10.1038/40446
  • Primary Citation of Related Structures:  
    1FOK

  • PubMed Abstract: 
  • FokI is a member of an unusual class of bipartite restriction enzymes that recognize a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence. Because of its unusual bipartite nature, FokI has been used to create artificial enzymes with new specificities ...

    FokI is a member of an unusual class of bipartite restriction enzymes that recognize a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence. Because of its unusual bipartite nature, FokI has been used to create artificial enzymes with new specificities. We have determined the crystal structure at 2.8A resolution of the complete FokI enzyme bound to DNA. As anticipated, the enzyme contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP. The CAP core has been extensively embellished in the first two subdomains, whereas in the third subdomain it has been co-opted for protein-protein interactions. Surprisingly, the cleavage domain contains only a single catalytic centre, raising the question of how monomeric FokI manages to cleave both DNA strands. Unexpectedly, the cleavage domain is sequestered in a 'piggyback' fashion by the recognition domain. The structure suggests a new mechanism for nuclease activation and provides a framework for the design of chimaeric enzymes with altered specificities.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Restriction Endonuclease Foki Bound to DNA
      Hirsch, J.A., Wah, D.A., Dorner, L.F., Schildkraut, I., Aggarwal, A.K.
      (1997) FEBS Lett 403: 136

    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York 10032, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (FOKI RESTRICTION ENDONUCLEASE)C [auth A]576Planomicrobium okeanokoitesMutation(s): 0 
Gene Names: fokIRrfoKI
EC: 3.1.21.4
UniProt
Find proteins for P14870 (Planomicrobium okeanokoites)
Explore P14870 
Go to UniProtKB:  P14870
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*CP*GP*GP*AP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*AP*G P*TP*CP*A)-3')A [auth B]20Planomicrobium okeanokoites
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*TP*GP*AP*CP*TP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*T P*CP*CP*G)-3')B [auth C]20N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.296 
      • R-Value Work: 0.214 
      • R-Value Observed: 0.214 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 65.59α = 90
      b = 119.34β = 101.42
      c = 71.52γ = 90
      Software Package:
      Software NamePurpose
      PHASESphasing
      CCP4model building
      SOLOMONphasing
      X-PLORmodel building
      X-PLORrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      CCP4phasing
      X-PLORphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1997-12-03
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2021-06-30
        Changes: Data collection