Pathways & interactions
Restriction endonuclease EcoO109IR, catalytic domain superfamily (IPR012297)
Short name: EcoO109IR_cat_dom_sf
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:18.104.22.168) 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:22.214.171.124) activities.
- Type II enzymes (EC:126.96.36.199) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
- Type III enzymes (EC:188.8.131.52) 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:184.108.40.206).
- Type IV enzymes target methylated DNA.
Type II restriction endonucleases (EC:220.127.116.11) 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 superfamily represents the catalytic domain of the restriction endonuclease EcoO109IR, which recognises the DNA sequence RGGNCCY. The catalytic domain of this endonuclease moves drastically to capture the DNA. EcoO109IR requires a metal ion, which acts as a Lewis acid to stabilise the pentavalent phosphorus atom in the transition state. EcoO109I is similar to EcoRI family enzymes in terms of its DNA cleavage pattern and folding topology of the common motif in the catalytic domain, but it differs in the manner of DNA recognition [PMID: 15590682].
- G3DSA:3.40.1560.10 (G3DSA:3.40.1560.10)