The enzyme FokI, naturally found in Flavobacterium

Flavobacterium

Flavobacterium is a genus of Gram-negative, non-motile and motile, rod-shaped bacteria that consists of ten recognized species, as well as three newly proposed species . Flavobacteria are found in soil and fresh water in a variety of environments...

 okeanokoites, is a bacterial type IIS restriction endonuclease consisting of an N-terminal DNA-binding domain

DNA-binding domain

A DNA-binding domain is an independently folded protein domain that contains at least one motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA sequence or have a general affinity to DNA...

 and a non-specific DNA cleavage domain at the C-terminal. Once the protein is bound to duplex

Duplex

Duplex commonly means double or twofold.It may also refer to:* Duplex , a two-unit apartment building or condominium* Duplex, a common electrical receptacle with two NEMA type 5 plugs* Duplex locomotive, a type of steam locomotive...

 DNA via its DNA-binding domain at the 5'-GGATG-3': 5'-CATCC-3' recognition site, the DNA cleavage domain is activated and cleaves, without further sequence specificity, the first strand 9 nucleotide

Nucleotide

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...

s downstream and the second strand 13 nucleotides upstream of the nearest nucleotide of the recognition site.

Its molecular mass

Molecular mass

The molecular mass of a substance is the mass of one molecule of that substance, in unified atomic mass unit u...

 is 65.4 kDa, being composed of 587 amino acids.

DNA-binding domain

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.

DNA-cleavage domain

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

Activity

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 dimerisation, when the recognition domain is bound to its cognate site and in the presence of magnesium ions.

Exploitation

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

Zinc finger

Zinc fingers are small protein structural motifs that can coordinate one or more zinc ions to help stabilize their folds. They can be classified into several different structural families and typically function as interaction modules that bind DNA, RNA, proteins, or small molecules...

 (see zinc finger nuclease

Zinc finger nuclease

Zinc-finger nucleases are artificial restriction enzymes generated by fusing a zinc finger DNA-binding domain to a DNA-cleavage domain. Zinc finger domains can be engineered to target desired DNA sequences and this enables zinc-finger nucleases to target unique sequences within complex genomes...

).

One of several human vitamin D receptor

Calcitriol receptor

The calcitriol receptor, also known as the vitamin D receptor and also known as NR1I1 , is a member of the nuclear receptor family of transcription factors...

 gene variants is a single nucleotide polymorphism

Single nucleotide polymorphism

A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes in an individual...

in the start codon of the gene which can be distinguished through the use of the FokI enzyme.