Pathways & interactions
Restriction endonuclease, type II, Cfr10I/Bse634I (IPR012415)
Short name: Restrct_endonuc_II_Cfr10I
Overlapping homologous superfamilies
- Restriction endonuclease type II-like (IPR011335)
There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [PMID: 15121719, PMID: 12665693], as summarised below:
- Type I enzymes (EC:22.214.171.124) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (EC:126.96.36.199) activities.
- Type II enzymes (EC:188.8.131.52) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
- Type III enzymes (EC:184.108.40.206) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (EC:220.127.116.11).
- Type IV enzymes target methylated DNA.
Type II restriction endonucleases (EC:18.104.22.168) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin [PMID: 15770420]. However, there is still considerable diversity amongst restriction endonucleases [PMID: 14576294, PMID: 11827971]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone [PMID: 11557805].
This entry represents Cfr10I and Bse634I restriction endonucleases. They exhibit a conserved tetrameric architecture that is of functional importance, wherein two dimers are arranged, back-to-back, with their putative DNA-binding clefts facing opposite directions. These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet. The monomer may be split into separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3 [PMID: 11842098]. Both Cfr10I and Bse634I recognise the double-stranded sequence RCCGGY and cleave after the purine R [PMID: 8568865].
- PF07832 (Bse634I)