Editing Restriction enzyme (section)

=== Type II ===
{{Infobox protein family
| Name = Type II site-specific deoxyribonuclease-like
|Symbol= Restrct_endonuc-II-like
| EC_number = 3.1.21.4
| CAS_number = 9075-08-5
| IUBMB_EC_number = 3/1/21/4
| footnote = GO:0009036
| image = 1QPS.png
| width =
|InterPro=IPR011335
|Pfam_clan=CL0236
|SCOP=1wte
| caption = Structure of the [[protein dimer|homodimeric]] restriction enzyme [[EcoRI]] (cyan and green cartoon diagram) bound to double stranded [[DNA]] (brown tubes).<ref name="pdb_1qps">{{PDB|1qps}} {{cite book |vauthors=Gigorescu A, Morvath M, Wilkosz PA, Chandrasekhar K, Rosenberg JM | editor = Alfred M. Pingoud | title = Restriction Endonucleases (Nucleic Acids and Molecular Biology, Volume 14) | publisher = Springer | location = Berlin | year = 2004 | chapter = The integration of recognition and cleavage: X-ray structures of pre-transition state complex, post-reactive complex, and the DNA-free endonuclease | pages = 137–178 | isbn = 3-540-20502-0 }}</ref> Two catalytic [[magnesium]] ions (one from each [[monomer]]) are shown as magenta spheres and are adjacent to the cleaved sites in the DNA made by the enzyme (depicted as gaps in the DNA backbone).
}}
Typical type II restriction enzymes differ from type I restriction enzymes in several ways. They form [[homodimer]]s, with recognition sites that are usually undivided and palindromic and 4–8 nucleotides in length. They recognize and cleave DNA at the same site, and they do not use ATP or AdoMet for their activity—they usually require only Mg<sup>2+</sup> as a cofactor.<ref name="pmid11557805"/>  These enzymes cleave the phosphodiester bond of double helix DNA. It can either cleave at the center of both strands to yield a blunt end, or at a staggered position leaving overhangs called sticky ends.<ref>{{Cite book|title=Fundamental Laboratory Approaches for Biochemistry and Biotechnology| vauthors = Ninfa JP, Balou DP, Benore M |publisher=John Wiley & Sons|year=2010|isbn=978-0-470-08766-4|location=Hoboken, NJ|pages=341}}</ref> These are the most commonly available and used restriction enzymes. In the 1990s and early 2000s, new enzymes from this family were discovered that did not follow all the classical criteria of this enzyme class, and new subfamily [[nomenclature]] was developed to divide this large family into subcategories based on deviations from typical characteristics of type II enzymes.<ref name="pmid11557805"/> These subgroups are defined using a letter suffix.

Type IIB restriction enzymes (e.g., BcgI and BplI) are [[multimer]]s, containing more than one subunit.<ref name="pmid11557805"/> They cleave DNA on both sides of their recognition to cut out the recognition site. They require both AdoMet and Mg<sup>2+</sup> cofactors. Type IIE restriction endonucleases (e.g., NaeI) cleave DNA following interaction with two copies of their recognition sequence.<ref name="pmid11557805"/> One recognition site acts as the target for cleavage, while the other acts as an [[Allosteric regulation|allosteric effector]] that speeds up or improves the efficiency of enzyme cleavage. Similar to type IIE enzymes, type IIF restriction endonucleases (e.g. NgoMIV) interact with two copies of their recognition sequence but cleave both sequences at the same time.<ref name="pmid11557805"/> Type IIG restriction endonucleases (e.g., RM.Eco57I) do have a single subunit, like classical Type II restriction enzymes, but require the cofactor AdoMet to be active.<ref name="pmid11557805"/> Type IIM restriction endonucleases, such as [[DpnI]], are able to recognize and cut methylated DNA.<ref name="pmid11557805"/><ref>{{cite journal | vauthors = Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K | title = Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI | journal = Nucleic Acids Research | volume = 40 | issue = 15 | pages = 7563–72 | date = August 2012 | pmid = 22610857 | pmc = 3424567 | doi = 10.1093/nar/gks428 }}</ref><ref>{{cite journal | vauthors = Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M | display-authors = 6 | title = Structural basis of the methylation specificity of R.DpnI | journal = Nucleic Acids Research | volume = 42 | issue = 13 | pages = 8745–54 | date = July 2014 | pmid = 24966351 | pmc = 4117772 | doi = 10.1093/nar/gku546 }}</ref> Type IIS restriction endonucleases (e.g. FokI) cleave DNA at a defined distance from their non-palindromic asymmetric recognition sites;<ref name="pmid11557805"/> this characteristic is widely used to perform in-vitro cloning techniques such as [[Golden Gate Cloning|Golden Gate cloning]]. These enzymes may function as [[protein dimer|dimer]]s. Similarly, Type IIT restriction enzymes (e.g., Bpu10I and BslI) are composed of two different subunits. Some recognize palindromic sequences while others have asymmetric recognition sites.<ref name="pmid11557805"/>
{{Further|BsuBI/PstI restriction endonuclease}}