Bgl II

          Bgl II is a restriction endonuclease, meaning that it cleaves a specific section of DNA. Bgl II is made up of two units; together the units encircle the DNA.

DNA is depicted in blue and Bgl II is orange

DNA is Blue and each unit it a different shade of orange

Bgl II, as well as Bgl I, were first discovered in Baccillus globigii, and were found useful in recombinant DNA experiment. Bgl II has 223 amino acids and each unit has two loops that enclose the DNA.

From this angle, the loops depicted in dark orange are visibly interacting

  Collectively in the entire interaction with DNA, there are 5 carbon bonds with the minor groove and 14 hydrogen bonds to the major groove.

 

          Bgl II scans the DNA from the major groove side and approaches the DNA from the major groove side. The enzyme uses a scissor like motion to bind with the DNA unlike other type two endonuclease restriction enzymes in its classification. When it is in the relaxed free position, the enzyme looks like this:

When Bgl II is bound to DNA it is in this position:

In addition to the scissor like motion, the loops that enclose the DNA are bent back in the free position, then bend over the DNA when Bgl II is interacting with the DNA.

          Ions present in solution with Bgl II are important to the activity. The ion Mg ²⁺ activates Bgl II the most, and the presence of NaCl aids in the activity.
      

          Bgl II binds and cleaves the same section of DNA as Bgl I. Type two restriction endonucleases cleave DNA without the use of ATP. Bgl II specifically cleaves a section leaving sticky ends. The place where the DNA is broken is marked with orange arrows in the picture below:

Bgl II does not significantly unwind the DNA when they are interacting and cleaves both Strands of DNA simultaneously, which is not common for restriction endonucleases.

          Bgl II is used in various experiments. One use is to break down large segments of DNA to be analyzed with Gel Electrophoresis. Also with this use, it is possible to determine if the site exists that Bgl II cleaves by seeing if the DNA traveled on the Gel; if there are multiple places where Bgl II cleaves, then there would be multiple small fragments. Endonuclease restriction enzymes are commonly used in Biotechnology experiments. Specifically, Bgl II is used in the insertion of gene segments into a section of DNA, such as a plasmid, or the deletion of a segment. This use of Bgl II is important in the replication of genes and the study of the results of changing DNA sequences.

 

The funny thing when talking about this protein is what do you call it: Bgl II

Photos taken from various blog posts then edited for resulting pictures

(All images were created for this page. The last image was two pictures taken from various blogs, then edited for this blog)


References:

• Lukacs, Christine M., Rebecca Kucera, Ira Schildkraut, and Aneel k. Aggarwal. "Structure of Free BglII reveals an unpredicted scissor-like motion for opening and endonuclease." Nature Publishing Group 8.2 (2001). Print.
  Structural Biology Program, Department of Physiology and Biophysics, Mount  Sinai School of Medicine
   

• Imber, Roland, and Thomas A. Bickle. "Purification and Properties of the Restriction Endonuclease BglII from Baccillus globigii." Federation of the Societies of Biochemistry and Molecular Biology 117 (1981): 395-99. Print.
  Microbiology Department, Biozentrum, University of Basel
   

• Pingoud, Alfred, and Albert Jeltsch. "Structure and Function of Type 2 Restricstion Endonucleases." Nucleic Acids Reasearch 29.18 (2001): 3705-27. Print.
  Institut für Biochemie (FB 08), Justus-Leibig-Univerität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany

Articles

Article Summaries:

Structure and Function of Type 2 restriction endonucleases

               Currently, there are more than 3000 type 2 restriction endonucleases discovered.  Restriction enzymes cleave specific regions of DNA. Specifically, type 2 restriction endonucleases do not require ATP Hydrolysis and there are also subdivisions that are more specific categories. Bgl2 is part of the EcoRI family as a sub category for type 2 restriction endonucleases. The sequence cleaved by Bgl2 is  AGATCT, and when it cleaves, there are sticky ends.  The binding site of Bgl2 encircles the DNA and approaches from the major groove side of the DNA and it also comes in contact with the minor groove side.  This article also goes into the specific residues that interact with each part of the DNA. Collectively in the entire interaction with DNA, there are 5 carbon bonds with the minor groove and 14 hydrogen bonds to the major groove.  “Altogether there are 28 backbone contacts, 20 of them are water-mediated”

Pingoud, Alfred, and Albert Jeltsch. "Structure and Function of Type 2 Restricstion Endonucleases." Nucleic Acids Reasearch 29.18 (2001): 3705-27. Print.

Institut für Biochemie (FB 08), Justus-Leibig-Univerität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany

Purification and Properties of the Restriction Endonuclease BglII from Baccillus globigii

               BglI and BglII were first discovered in Baccillus globigii and found to be useful  in recombinant DNA experiments. Both BglI and BglII recognize the same section of DNA.  This paper discusses the purification of BglII and properties discovered for BglII. For enzymatic activity for BglII, Magnesium must be present. Sodium Chloride is also required for some stimulation of enzymatic activity. The researchers found that the optimum pH is higher than most other restrictions enzymes, but they also say that this optimum might be different when other labs research it.  They tested other ions to see if they would activate enzymatic activity and the ones that did were Mn²⁺, Zn²⁺, Cd²⁺, and Ni²⁺; and Mn²⁺ was observed to be better than low concentrations of Mg²⁺.  They also looked at the interactions with DNA. They found that BglII does not significantly unwind DNA and that it cleaves both strands almost simultaneously.

Imber, Roland, and Thomas A. Bickle. "Purification and Properties of the Restriction Endonuclease BglII from Baccillus globigii." Federation of the Societies of Biochemistry and Molecular Biology 117 (1981): 395-99. Print.

Microbiology Department, Biozentrum, University of Basel

Structure of Free BglII reveals an unpredicted scissor-like motion for opening and endonuclease

               This article analyses the movement of BglII in a scissor like motion. BgkII has 223 amino acids in its structure and it is a dimer, made up of two units. Each unit has two loops that enclose the DNA by reaching around the minor groove. The active site residues are only exposed for catalysis when a group called the lever is in the up position, interacting with the DNA.

Lukacs, Christine M., Rebecca Kucera, Ira Schildkraut, and Aneel k. Aggarwal. "Structure of Free BglII reveals an unpredicted scissor-like motion for opening and endonuclease." Nature Publishing Group 8.2 (2001). Print.

Structural Biology Program, Department of Physiology and Biophysics, Mount  Sinai School of Medicine

BglII Pictures

The green is the protein BGL 2 and the orange and blue is a DNA molecule. From this angle you can see that loops of BGL 2 are in the grooves of the DNA molecule.

BGL 2 is represented with spheres color coed by element.

BGL 2 as spheres and each color is an individual chain in BGL 2

BGL 2 and DNA, green and blue,  looking down the DNA

Another view of BGL 2 loops interacting with DNA

BGL 2 shown in black looking at interaction with DNA

A view of the back of the BGL 2 with Helix, red; sheet, yellow; and loop, green, color scheme