Type IIS restriction endonuclease FokI is a member of an unusual class of bipartite restriction enzymes that recognises the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand [1]. FokI 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 [3]. This entry represents the subdomain D2 of FokI. D1 and D2 make almost all of the base-specific contacts with the DNA [3].

1: Structure of FokI has implications for DNA cleavage. Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK; Proc Natl Acad Sci U S A. 1998;95:10564-10569. PMID:9724743

2: Type II restriction endonucleases: structural, functional and evolutionary relationships. Kovall RA, Matthews BW; Curr Opin Chem Biol 1999;3:578-583. PMID:10508668

3: Structure of the multimodular endonuclease FokI bound to DNA. Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK; Nature. 1997;388:97-100. PMID:9214510