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Restriction endonuclease FokI, C terminal
Restriction endonuclease FokI bound to DNA PDB 1fok [1]
Symbol Endonuc-FokI_C
Pfam PF09254
Pfam clan CL0415
InterPro IPR015334
SCOP 2fok

The enzyme FokI, naturally found in Flavobacterium okeanokoites, is a bacterial type IIS restriction endonuclease consisting of an N-terminal DNA-binding domain and a non-specific DNA cleavage domain at the C-terminal.[2] Once the protein is bound to duplex DNA via its DNA-binding domain at the 5'-GGATG-3' recognition site, the DNA cleavage domain is activated and cleaves, without further sequence specificity, the first strand 9 nucleotides downstream and the second strand 13 nucleotides upstream of the nearest nucleotide of the recognition site.[3]

Its molecular mass is 65.4 kDa, being composed of 587 amino acids.

DNA-binding domain[edit]

The recognition domain contains three subdomains (D1, D2 and D3) that are evolutionarily related to the DNA-binding domain of the catabolite gene activator protein which contains a helix-turn-helix.[3]

DNA-cleavage domain[edit]

DNA cleavage is mediated through the non-specific cleavage domain which also includes the dimerisation surface.[4] The dimer interface is formed by the parallel helices α4 and α5 and two loops P1 and P2 of the cleavage domain.[3]


When the nuclease is unbound to DNA, the endonuclease domain is sequestered by the DNA-binding domain and is released through a conformational change in the DNA-binding domain upon binding to its recognition site. Cleavage only occurs upon dimerization, when the recognition domain is bound to its cognate site and in the presence of magnesium ions.[4]


The endonuclease domain of FokI has been used in several studies, after combination with a variety of DNA-binding domains such as the zinc finger (see zinc finger nuclease),[2] or inactive Cas9[5][6][7]

One of several human vitamin D receptor gene variants is caused by a single nucleotide polymorphism in the start codon of the gene which can be distinguished through the use of the FokI enzyme.[8]


  1. ^ Aggarwal, A. K.; Wah, D. A.; Hirsch, J. A.; Dorner, L. F.; Schildkraut, I. (1997). "Structure of the multimodular endonuclease FokI bound to DNA". Nature. 388 (6637): 97–100. doi:10.1038/40446. PMID 9214510. 
  2. ^ a b Durai S, Mani M, Kandavelou K, Wu J, Porteus M, Chandrasegaran S (2005). "Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells". Nucleic Acids Res. 33 (18): 5978–90. doi:10.1093/nar/gki912. PMC 1270952Freely accessible. PMID 16251401. 
  3. ^ a b c Wah, D. A.; Bitinaite, J.; Schildkraut, I.; Aggarwal, A. K. (1998). "Structure of FokI has implications for DNA cleavage". Proc Natl Acad Sci USA. 95 (18): 10564–9. doi:10.1073/pnas.95.18.10564. PMC 27934Freely accessible. PMID 9724743. 
  4. ^ a b Bitinaite, J.; Wah, D. A.; Aggarwal, A. K.; Schildkraut, I. (1998). "FokI dimerization is required for DNA cleavage". Proc Natl Acad Sci USA. 95 (18): 10570–5. doi:10.1073/pnas.95.18.10570. PMC 27935Freely accessible. PMID 9724744. 
  5. ^ Tsai, S. Q. et al. (2014). Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nature Biotechnol. 32, 569–576 doi:10.1038/nbt.2908
  6. ^ Guilinger, J. P., Thompson, D. B. & Liu, D. R. (2014). Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nature Biotechnol. 32, 577–582 doi:10.1038/nbt.2909
  7. ^ Wyvekens, N., Topkar, V. V., Khayter, C., Joung, J. K. & Tsai, S. Q. (2015). Dimeric CRISPR RNA-guided FokI-dCas9 nucleases directed by truncated gRNAs for highly specific genome editing. Hum. Gene Ther. 26, 425–431 doi:10.1089/hum.2015.084
  8. ^ Strandberg, S.; et al. (2003). "Vitamin D receptor start codon polymorphism (FokI) is related to bone mineral density in healthy adolescent boys". J Bone Miner Metab. 21 (2): 109–13. doi:10.1007/s007740300018. PMID 12601576. 

See also[edit]