1FOK

STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 creat ...

    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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (FOKI RESTRICTION ENDONUCLEASE)
A
576Planomicrobium okeanokoitesGene Names: fokIR (rfoKI)
EC: 3.1.21.4
Find proteins for P14870 (Planomicrobium okeanokoites)
Go to UniProtKB:  P14870
Entity ID: 1
MoleculeChainsLengthOrganism
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')B20Planomicrobium okeanokoites
Entity ID: 2
MoleculeChainsLengthOrganism
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')C20N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.590α = 90.00
b = 119.340β = 101.42
c = 71.520γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLOMONphasing
PHASESphasing
X-PLORmodel building
CCP4model building
X-PLORrefinement
SCALEPACKdata scaling
CCP4phasing
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-03
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance