The key difference between type 1 2 and 3 restriction endonuclease is that the cleavage site of type 1 restriction endonuclease is random and is away from the recognition site, while the cleavage site of type 2 restriction endonuclease is at the recognition site and the cleavage site of type 3 restriction endonuclease is 20-30 base pairs downstream of the recognition site.
Restriction endonuclease or restriction enzyme is an enzyme that helps to cleave DNA into fragments at or near specific recognition sites within molecules known as restriction sites. They fall into the class of broader endonuclease group enzymes. Restriction endonucleases are commonly classified into five types according to their structures, the specific recognition site at which they cut their DNA substrate, and based on if the recognition and cleavage sites are separated from each other or not. In order to cut or cleave DNA, all restriction enzymes produce two incisions, once through each sugar-phosphate backbone of the DNA double helix. Restriction enzymes are present in bacteria and archaea to provide defense mechanisms against the invasions of viruses.
CONTENTS
1. Overview and Key Difference
2. What is Type 1 Restriction Endonuclease
3. What is Type 2 Restriction Endonuclease
4. What is Type 3 Restriction Endonuclease
5. Similarities – Type 1 2 and 3 Restriction Endonuclease
6. Type 1 vs 2 vs 3 Restriction Endonuclease in Tabular Form
7. Summary – Type 1 vs 2 vs 3 Restriction Endonuclease
What is Type 1 Restriction Endonuclease?
Type 1 restriction endonuclease is an enzyme complex with both restriction and methylase activities. It is identified in two different strains of E. coli. Type 1 restriction enzymes cut at a site that differs and is a random distance away from the recognition site. The cleavage at these random sites follows a DNA translocation process. These enzymes are multifunctional and have the ability for both restriction digestion and modification activities depending on the methylation status of the targeted DNA. The co-factors S-Adenosyl methionine (AdoMet), hydrolyzed adenosine triphosphate (ATP), and magnesium ions (Mg 2+) are essential for their full activity.
Type 1 restriction enzymes are composed of three subunits called HsdR, HsdM, and HsdS. HsdR is required for restriction digestion. HsdM is required for the addition of methyl groups to host DNA. This process is known as methyltransferase activity. HsdS is required for the recognition of specific DNA binding sites. It is also important in restriction digestion as well as methyltransferase activity.
What is Type 2 Restriction Endonuclease?
Type 2 restriction endonuclease is a type of restriction enzyme that helps in cleaving DNA at specific positions, either within or close to the restriction recognition site. They form homodimers with recognition sites that are undivided and palindromic, with four to eight nucleotides in length. Type 2 restriction enzymes do not require ATP or AdoMet for their activity, but Mg2+ is required as a cofactor. These enzymes help in the cleavage of phosphodiester bonds of double helix DNA. They cleave at the center of both strands in order to yield a blunt end or cleave at a staggered position leaving the overhangs that are known as sticky ends.
Type 2 restriction endonucleases are the most commonly available restriction enzyme since they produce discrete fragments by restriction digestion by cutting specifically at or close to the recognition site. Type 2 restriction endonucleases belong to a large family; hence, they are divided into subfamilies based on the deviation from the typical characteristics of these enzymes. These subcategories include type 2B, 2E, 2F, 2G, 2S, and 2T.
What is Type 3 Restriction Endonuclease?
Type 3 restriction endonuclease is a type of restriction enzyme that recognizes two separate non-palindromic sequences that are oriented inversely. They usually cleave DNA of about 20-30 base pairs downstream of the recognition site. These enzymes consist of more than one subunit. They also require ATP and AdoMet for their activity. Type 3 restriction enzymes are essential in the mechanisms of prokaryotic DNA restriction modification. These enzymes help protect the organism against invading foreign DNA.
Type 3 enzymes are hetero-oligomeric and multifunctional proteins composed of two subunits. They are Res and Mod. Res subunit is important in restriction digestion; however, it has no enzymatic activity on its own. Mod subunit helps in the recognition of DNA sequences that are specific to the system and is a modification methyltransferase. Type 3 restriction enzymes also recognize 5-6 base pair long asymmetric DNA sequences and cleave 25-27 base pairs downstream to leave short single-stranded 5’ protrusions. These enzymes methylate only one strand of the DNA and are sufficient to protect against restriction digestion.
What are the Similarities Between Type 1 2 and 3 Restriction Endonuclease?
- Type 1, type 2, and type 3 restriction endonuclease are three restriction enzymes.
- They are responsible for the cleaving of DNA at specific sites called restriction recognition sites within the molecule.
- They belong to a broader class of endonuclease.
- They make two incisions, once in each of the two sugar-phosphate backbones of the DNA double helix.
- They are present in bacteria and archaea.
- Moreover, they help to protect against invading viruses.
- All three enzymes have the ability for both restriction digestion and methyltransferase activity.
- The restriction enzymes cut foreign DNA through restriction digestion.
- Methyltransferase is the modification enzyme present in all three enzymes.
What is the Difference Between Type 1 2 and 3 Restriction Endonuclease?
The cleavage site of type 1 restriction endonuclease is random and away from the recognition site, while in type 2 restriction endonuclease, it is at the recognition site. Whereas, in type 3 restriction endonuclease, the cleavage site is 20-30 base pairs downstream of the recognition site. Thus, this is the key difference between type 1 2 and 3 restriction endonuclease. Moreover, type 1 restriction endonuclease consists of three subunits and is considered a bifunctional enzyme with both restriction and methylase activities. Type 2 restriction endonuclease consists of two subunits and has separate restriction and methylase activities. And, type 3 restriction endonuclease consists of more than one subunit, usually two, and is also a bifunctional enzyme with both restriction and methylase activities.
The below infographic presents the differences between type 1 2 and 3 restriction endonuclease in tabular form for side-by-side comparison.
Summary – Type 1 vs 2 vs 3 Restriction Endonuclease
Restriction endonuclease helps to cleave DNA into fragments at or near specific recognition sites within molecules. Type 1, type 2 and type 3 restriction endonuclease are three restriction enzymes. The cleavage site of type 1 restriction endonuclease is random and away from the recognition site. The cleavage site of type 2 restriction endonuclease is at the recognition site, while the cleavage site of type 3 restriction endonuclease is 20-30 base pairs downstream of the recognition site. So, this summarizes the difference between type 1 2 and 3 restriction endonuclease.
Reference:
1. Loenen, W. A., et al. “Type I Restriction Enzymes and Their Relatives.” Nucleic Acids Research, vol. 42, no. 1, 2013, pp. 20–44.
2. Rao, Desirazu N., et al. “Type III Restriction-Modification Enzymes: A Historical Perspective.” Nucleic Acids Research, vol. 42, no. 1, 2013, pp. 45–55.
3. “Restriction Endonucleases.” An Overview | ScienceDirect Topics.
Image Courtesy:
1. “Steps of Molecular Cloning” By Alexpicardal97 – Own work (CC BY-SA 4.0) via Commons Wikimedia
2. “HindIII Restriction site and sticky ends vector” By Helixitta – Own work (CC BY-SA 4.0) via Commons Wikimedia
3. “Restriction Fragment Length Polymorphism” By Lolyas39 – Own work (CC BY-SA 4.0) via Commons Wikimedia