What is the Difference Between Restriction Enzymes Type 1 2 and 3

The main difference between restriction enzymes type 1, 2, and 3 is that restriction enzyme type 1 and 2 enzymes have both restriction and methylase activities in one large enzyme complex, whereas restriction enzyme type 2 has independent restriction and methylase activities. Furthermore, restriction enzyme type 1 and 3 cleave DNA randomly, sometimes hundreds of bases away from restriction site while restriction enzyme type 2 cleaves DNA at specific sites within the restriction recognition site.  

Restriction enzymes type 1, 2, and 3 are three of the five types of restriction enzymes responsible for cleaving DNA at specific sites within the molecule known as restriction recognition sites. Generally, they are a broad class of endonucleases mainly produced by prokaryotes. 

Key Areas Covered 

1. What is Restriction Enzyme Type 1
     – Definition, Structure, Function
2. What is Restriction Enzyme Type 2
     – Definition, Structure, Function
3. What is Restriction Enzyme Type 3
     – Definition, Structure, Function
4. What are the Similarities Between Restriction Enzymes Type 1 2 and 3
     – Outline of Common Features
5. What is the Difference Between Restriction Enzymes Type 1 2 and 3
     – Comparison of Key Differences

Key Terms 

Endonucleases, Restriction Enzymes Type 1, 2, and 3, Restriction Recognition Sites

Whats is Restriction Enzyme Type 1 

Restriction enzyme type 1 is a complex, multisubunit enzyme with both restriction and methylase activities in combination. Also, it was first identified in E. coli strains. Besides, it composes of three different subunits; HsdR, HsdM, and HsdS Here, HsdR undergoes restriction digestion, HsdM undergoes methylation, and HsdS is important for the recognition of both the recognition site and methylation sites. 

Figure 1: EcoR I Homodimeric Structure

Furthermore, restriction enzyme 1 cleaves DNA at a site, which is at a random distance of more than 1000 bp away from the restriction recognition site. Also, this random cleavage is followed by DNA translocation as this enzyme serves as a molecular motor. On the other hand, restriction enzyme 1 genes are more common in the prokaryotic genome. However, although restriction enzyme type 1 has biochemical importance, it has a little practical value due to the production of discrete restriction fragments. 

What is Restriction Enzyme Type 2 

Restriction enzyme type 2 is another type of restriction enzymes, cleaving DNA at defined positions, which are either within or close to the restriction recognition site. Also, its recognition site is palindromic and 4-8 nucleotides in length. Generally, it is a homodimer with independent restriction and methylase activities. On the other hand, it only requires magnesium as a cofactor without using ATP.

Figure 2: EcoR I Restriction Recognition Site

Moreover, due to the production of discrete fragments by restriction digestion by cutting specifically at or close to the recognition site, restriction enzyme type 2 is more often used in laboratories for DNA analysis and cloning. For instance, restriction enzyme type 2 has several families with completely different structures. They include restriction enzyme type 2B, 2E, 2F, 2G, 2S, and 2T. 

What is Restriction enzyme Type 3 

Restriction enzyme type 3 is the third type of restriction enzymes, recognizing two separate non-palindromic sequences, which are inversely oriented. Also, it cleaves DNA about 20-30 bp downstream to the recognition site. Generally, restriction enzyme type 3 is a heterodimer with two different subunits. 

Figure 3: Role in Restriction Enzymes in Cloning

In the meanwhile, the restriction and methylation activities occur in the same subunit of the restriction enzyme type 3. However, it rarely gives complete digestion. 

Similarities Between Restriction Enzymes Type 1 2 and 3 

• Restriction enzymes type 1, 2, and 3 are three of the five restriction enzymes responsible for cleaving DNA at specific sites within the molecule known as restriction recognition sites. 
• They are a broad class of endonucleases. 
• Each type differs from its structure and the type of cleavage. 
• They make two incisions once in each of the two sugar-phosphate backbones of the DNA double helix. 
• Both bacteria and archaea in order to provide defense against invading viruses. 
• Inside bacteria, these restriction enzymes cut foreign DNA in a process known as restriction digestion.  
• Apart from the restriction enzymes, methyltransferase is the modification enzyme, which protects host DNA from restriction cleavage by the methylation of DNA at the host specificity site. Significantly, both enzymes are in the restriction-modification system of prokaryotes. 
• There are around 600 restriction enzymes are commercially available and are routinely used in laboratories for DNA modification in techniques, including molecular cloning. 

Difference Between Restriction Enzymes Type 1 2 and 3 

Definition 

Restriction enzyme type 1 refers to a complex, multisubunit, combination of restriction-and-modification enzymes, which cut DNA at random far from their recognition sequences. Restriction enzyme type 2 refers to the enzymes, which cut DNA at defined positions close to or within their recognition sequences. On the other hand, the restriction enzyme type 3 refers to a large combination of restriction-and-modification enzymes, which cleave outside of their recognition sequences, rarely giving a complete digest. 

Subunits 

Restriction enzyme type 1 contains three subunits, restriction enzyme type 2 is a homodimer with two subunits, while restriction enzyme type 3 also contains more than one subunit, usually two. 

Structure

Structurally, the restriction enzyme type 1 is a bifunctional enzyme with both restriction and methylase activities. The restriction enzyme type 2 has separate restriction and methylase activities. Meanwhile, the restriction enzyme type 3 is also a bifunctional enzyme with both restriction and methylase activities. 

Restriction and Methylation 

Importantly, restriction and methylation are naturally exclusive in restriction enzyme type 1, while restriction and methylation are two separate reactions in restriction enzyme type 2. But, restriction and methylation are simultaneous reactions in restriction enzyme type 3. 

Restriction Recognition Site 

Restriction enzyme type 1 has a bipartite and asymmetric restriction recognition site. Meanwhile, restriction enzyme type 2 has a 4-6 bp palindromic sequence. On the other hand, the restriction enzyme type 3 has a 5-7 bp asymmetric restriction recognition site. 

Cleavage Site 

The cleavage site is nonspecific, >1000 bp from recognition site in restriction enzyme type 1, the cleavage site is the same as or close to the recognition site, while the cleavage site is 24-26 bp downstream of the recognition site. 

Restriction Requirements 

ATP, Mg²⁺, and S-adenosyl methionine are the requirements of restriction enzyme type 1, Mg²⁺ is the requirement for restriction enzyme type 2, while ATP and Mg²⁺ are the requirements of restriction enzyme type 3. 

DNA Translocation 

Cleavage is followed by DNA translocation in restriction enzyme type 1. However, DNA translocations occur in restriction enzyme type 2 and 3. 

Examples 

EcoA 1, EcoB, EcoK I, and CfrA I are the examples of restriction enzyme type 1, EcoR I BamH I, and Hind III are the examples of restriction enzyme type 2 while EcoP I, Hinf III, and EcoP15 I are the examples of restriction enzyme type 3. 

Conclusion 

Restriction enzyme type 1 is one of the types of restriction enzymes with both restriction and methylase activities in the same large complex of the enzyme. Generally, it composes of three different subunits. Also, its cleavage site is random and occurs around 1000 bp away from the recognition site. On the other hand, restriction enzyme type 2 is another type of restriction enzyme with independent restriction and methylase activities. Also, it is a homodimer, which cleaves DNA within or closely to the recognition site. Meanwhile, restriction enzyme type 3 is the third type of restriction enzyme. Importantly, it also has the restriction and methylase activities together. However, it is a heterodimer, which cleaves DNA randomly 24-26 bp away from the recognition site. Therefore, the main difference between restriction enzyme type 1, 2, and 3 is their structure and the pattern of cleavage. 

References:

1. “Types of Restriction Endonucleases.” NEB, New England Biolabs, Available Here.

Image Courtesy:

1. “1QPS” By Boghog2 – Own workThis structure was created with PyMOL. (Public Domain) via Commons Wikimedia   
2. “EcoRI restriction enzyme recognition site” By User:Bryan Derksen – Own work (Public Domain) via Commons Wikimedia   
3. “Construct” By Joyxi – Own work (Public Domain) via Commons Wikimedia