Table 2.
Nomenclature of Type II restriction enzymes
| Subtype | Features of restriction enzymesa | Examples |
|---|---|---|
| Type IIP | Palindromic recognition sequence; recognized by both homodimeric and monomeric enzymes; cleavage occurs symmetrically, usually within the recognition sequence | Prototypes EcoRI & EcoRV |
| Type IIA | Asymmetric recognition sequence | FokI |
| Type IIB | Cleavage on both sides of the recognition sequence | BcgI |
| Type IIC | Single, combination R-M polypeptide | HaeIV |
| Type IIE | Two sequences required for cleavage, one serving as allosteric effector | EcoRII, Sau3AI |
| Type IIF | Two sequences required for cleavage, concerted reaction by homotetramer | SfiI |
| Type IIG | Requires AdoMet cofactor for both R-M | Eco57I |
| Type IIH | Separate M and S subunits; MTase organization similar to Type I systems | BcgI |
| Type IIM | Require methylated recognition sequence; Type IIP or Type IIA | DpnI |
| Type IIS | Asymmetric recognition sequence; cleavage at fixed positions usually outside recognition sequence | FokI |
| Type IIT | Heterodimeric restriction enzyme. | Bpu10I, BslI |
| Putatives | All subtypes | |
| Control | Control proteins of Type II restriction enzymes | C.BamHI, C.PvuII |
The characteristics of the orthodox Type IIP enzymes originally distinguished this group of enzymes from the Type I and III R-M systems. Type IIP is the largest group, owing to its valuable role in molecular science and its commercial value, but the current classification and growing number of R-M systems (putatively) identified, makes it clear that Type II enzymes are highly diverse and the boundaries with the other types are beginning to blur; see also Figure 3 and text for details.
aThese classifications reflect enzyme properties and activities, and not their evolutionary relationships. The classifications are not exclusive, and one enzyme can often belong several classes. Thus BcgI, for example, is Type IIA, B, C, G and H (see text for details).