Type II restriction endonuclease

Pingoud, A., Fuxreiter, M., Pingoud, V. and Wende, W. (2005) Type II restriction endonucleases structure and mechanism, Cell.Mol.Life Sci. 62, 685-707. 

The recognition sequences of type II restriction endonucleases are usually symmetric they have a twofold axis of symmetry so that they read the same in the 5 -to-3 sense along opposite—but, of course, complementary—strands. Such sequences are... 

Thousands of restriction endonucleases have been discovered in different bacterial species, and more than 100 different DNA sequences are recognized by one or more of these enzymes. The recognition sequences are usually 4 to 6 bp long and palindromic (see Fig. 8-20). Table 9-2 lists sequences recognized by a few type II restriction endonucleases. In some cases, the interaction between a restriction endonuclease and its target sequence has been elucidated in exquisite molecular detail for example, Figure 9-2 shows the complex of the type II restriction endonuclease EcoRV and its target sequence. 

TABLE 9-2 Recognition Sequences for Some Type II Restriction Endonucleases... 

The type II restriction endonucleases, which are the ones most widely used in molecular biology, are relatively small 50- to 100-kDa monomeric or dimeric proteins. About 2400 different enzymes with 188 different specificities had been isolated by 1995.83/84 The sites of attack, in most instances, are nucleotide sequences with a twofold axis of local symmetry.85 For example, the following sites of cleavage have been identified for two restriction endonucleases encoded by the DNA of R-factor plasmids of E. coli and for a restriction enzyme from Hemophilus influenzae. In the diagrams i are sites of cleavage, are sites of methyla-tion, and are local twofold axes (centers of palindromes) N can be any nucleotide with a proper base pairing partner. 

The recognition sequences of type II restriction endonucleases are shown with the arrow (J.) indicating the cleavage site. 

Type II restriction endonucleases recognize specific base sequences in double-stranded DNA, and cleave both strands of the duplex. More than 600 restriction endonucleases have been reported in the literature. Some 121 restriction endonucleases are listed in Current Protocols in Molecular Biology as commercially available ( 3). Table II, adapted from the 1988 Sigma Chemical Company Catalog, lists 35 of the endonucleases available from that source. Endonucleases are found in many bacteria where their function is to hydrolyze foreign DNA introduced by phage infection, conjugation or transformation. The first restriction endonucleases were discovered and isolated in 1968 (4,5). 

An interesting subgroup is represented by the type IIS restriction endonucleases. These enzymes recognize an asymmetric site and cleave this sequence at a defined distance after dimerizing on the substrate (for example FokI). 

Fig. 13.2. Cleavage of the specific recognition sites by the type II restriction endonucleases EcoRV, EcoRI and Bg/I The cleavage reaction, which requires Mg2+ as cofactor, leads to 5 phosphate and 3 OH ends. While EcoRV cleavage results in blunt ends, EcoRI and Bg/I generate sticky ends with a 5 and 3 overhang, respectively.

Setting the stage for protein engineering of type II restriction endonucleases... 

The extension of recognition sequences of type II restriction endonucleases also turned out to be a more than difficult job. The function of the different contacts within the protein DNA interface is still poorly understood, as is the mechanism of how... 

Fokl A type IIS restriction endonuclease derived from Flavobacterium okeanokoites... 

R. A. and Matthews, B.W., Type II restriction endonucleases structural, functional, and evolutionary relationships, Curr. Opin. Chem. Biol. 3, 578-583, 1999 Akar, A., Orkunoglu, F.E., Ozata, M., Sengul, A., and Gur, A.R., Lack of association between vitamin D receptor Fokl polymorphism and alopecia areata, Eur. J. Dermatol. 14, 156-158, 2004 Guy, M., Lowe, L.C., Bretherton-Watt, D. et al., Vitamin D receptor gene polymorphisms and breast cancer risk, Clin. Cancer Res. 10, 5472-5481, 2004 Claassen, M., Nouwen, J., Fang, Y. et al., Staphylococcus aureus nasal carriage is not associated with known polymorphism in the Vitamin D receptor gene, FEMS Immunol. Med. Microbiol. 43,173-176, 2005 Bolu,... 

Type II restriction enzymes are prevalent in Archaea and Eubacteria. What can we tell of the evolutionary history of these enzymes Comparison of the amino acid sequences of a variety of type II restriction endonucleases did not reveal significant sequence similarity between most pairs of enzymes. However, a carefiil examination of three-dimensional structures, taking into account the location of the active sites, revealed the presence of a core structure conserved in the different enzymes. This structure includes P strands that contain the aspartate (or, in some cases, glutamate) residues forming the magnesium ion binding sites (Figure 9.44). 

Type II restriction endonucleases (25) are enzymes isolated from procaryotes which recognize and make double-stranded cuts at specific DNA sequences. We investigated how platination of plasmid pBR322 would affect the ability of the enzyme Bam HI to cut at its single recognition sequence in this plasmid (23) Bam HI... 

The type II restriction endonucleases, which are the ones most widely used in molecular biology, are relatively small 50- to 100-kDa monomeric or dimeric proteins. About 2400 different enzymes with 188 different specificities had been isolated by 1995. ... 

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