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10  structures 69  species 1  interaction 70  sequences 2  architectures

Family: Endonuc-BglII (PF09195)

Summary: Restriction endonuclease BglII

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BglII Edit Wikipedia article

BglII recognition site. The scissile phoshodiester bonds between the Adenine and Guanine residues of both strands are hydrolyzed within the enzyme's active site. Mechanism shown below.
Restriction endonuclease BglII
PDB 2p0j EBI.jpg
structure of restriction endonuclease BstYI bound to non-cognate DNA
Symbol Endonuc-BglII
Pfam PF09195
Pfam clan CL0236
InterPro IPR015278
SCOP 1dfm

BglII (pronounced "begel two") is a type II restriction endonuclease enzyme isolated from certain strains of Bacillus globigii.

The principal function of restriction enzymes is the protection of the host genome against foreign DNA, but they may also have some involvement in recombination and transposition.[1]

Like most type II restriction enzymes, BglII consists of two identical subunits that form a homodimer around the DNA double helix. Each monomer is 223 amino acids and symmetrically bind both sides of the unique palindromic nucleotide sequence AGATCT, cleaving the scissile phosphodiester bond between the first Adenine and Guanine nucleotides on both strands of the DNA molecule, creating sticky ends with 5' end overhangs.

Being a type II restriction enzyme, BglII does not require ATP (adenosine triphosphate) for its enzymatic function, but only requires association with a divalent metal cation, most likely Mg2+. Unlike other restriction enzymes of its class, BglII has been show to possess some unique structural characteristics, such as a β-sandwich subdomain, and appears to undergo a unique conformational change upon dimerization,[2] but its overall structure and mechanism of catalysis remain consistent with other type II restriction enzymes.

Restriction Endonuclease enzymes play a very important role in modern molecular cloning techniques. Because of their unique recognition/cut sites, restriction enzymes can be used to precisely cut DNA in specific locations in a controllable manner. Once cut, scientist can then insert the desired DNA fragment possessing "sticky ends" into a circular DNA molecule, and ligate them together to create an engineered cloning vector.

Name BglII Restriction Endonuclease
Entrez 6173168
EC Number


BglII mechanism This phosphoryl transfer occurs by a nucleophilic attack of a hydride ion on the scissile phosphate, resulting in a trigonal bipyramidal phosphorus intermediate. The phosphorus then gets substituted and the 3'-0- is kicked off as a leaving group.

BglII catalyses phosphodiester bond cleavage at the DNA backbone through a phosphoryl transfer to water.[1] Studies on the mechanism of restriction enzymes have revealed several general features that seem to be true in almost all cases, although the actual mechanism for each enzyme is most likely some variation of this general mechanism. This mechanism requires a base to generate the hydroxide ion from water, which will act as the nucleophile and attack the phosphorus in the phosphodiester bond. Also required is a Lewis acid to stabilize the extra negative charge of the pentacoordinated transition state phosphorus, as well as a general acid or metal ion that stabilizes the leaving group (3’-O-).


PDB Code: 1DFM. Crystal Structure of BglII complexed with DNA at a resolution of 1.5Å [1]

Although restriction endonucleases show little sequence similarity, crystal structures reveal that they all share a highly similar α/β core consisting of a six-stranded β-sheet flanked by five α-helicies, two of which mediate dimerization.[1] This core carries the active site (catalytic center) and the residues that contact DNA in the major groove. BglII is unique in that its α/β core is augmented by a β-sandwich subdomain that has several projections that extend outward to grip the DNA, allowing BglII to completely encircle the DNA molecule. This atypical feature of BglII suggests a unique hinge motion for DNA binding and release.[2] Comparative structural studies of the free enzyme vs. the BglII-DNA complex showed that the enzyme opens by a dramatic scissor-like motion, accompanied by a complete rearrangement of the α-helicies at the dimer interface. These structural studies also revealed that within each monomer a set of residues lowers or raises to alternatively sequester or expose the active site residues. These dramatic differences in structure in the free vs. bound enzyme have yet to be observed in any other restriction endonuclease and may possibly represent a novel mechanism for capturing DNA that may extend to other proteins that encircle DNA.[2][3]

Active site

BglII active site residues coordinate with Mg2+ cation and water molecules to create the perfect conditions for enzymatic bond cleavage.[1][4] PDB: 1DFM

Structural studies of endonucleases have revealed a similar architecture for the [active site] with the residues following the weak consensus sequence (Glu/Asp)-X(9-20)-(Glu/Asp/Ser)-X-(Lys/Glu). BglII active site is similar to other endonucleases, but follows the sequence Asp 84-X9-Glu 93-X-Gln 95. In its active site there sits a divalent metal ion, most likely Mg2+, that allows interactions with Asp 84, Val 94, a phosphorus oxygen, and three water molecules. One of these water molecules, which we have labeled Nu, is well equipped to be the source of the hydroxide nucleophile because of its proximity to the scissile phosphate as well as a pKa lowered by its contact with the metal and its orientation fixed by a hydrogen bond with the side chain Oxygen of Gln 95.[1][4]

See also

  • BamHI, a nuclease enzyme from 'Bacillus amyloliquefaciens..
  • FokI, a nuclease enzyme from Flavobacterium okeanokoites
  • EcoRI, a nuclease enzyme from 'E. coli.


  1. ^ a b c d e f Lukacs; Kucera, R; Schildkraut, I; Aggarwal, AK; et al. (2000). "Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1,5 Å resolution.". Nature Structural & Molecular Biology. 7 (2): 134–40. doi:10.1038/72405. PMID 10655616. 
  2. ^ a b c Lukacs; Kucera, R; Schildkraut, I; Aggarwal, AK; et al. (2001). "Structure of free BglII reveals an unprecedented scissor-like motion for opening and endonuclease.". Nature Structural & Molecular Biology. 8 (2): 126–130. doi:10.1038/84111. PMID 11175900. 
  3. ^ Galburt, E. A.; Stoddard, B. L. (2000). "Restriction endonucleases: one of these things is not like the others.". Nature Structural & Molecular Biology. 7 (2): 89–91. doi:10.1038/72450. PMID 10655603. 
  4. ^ a b Pingoud, Alfred; Jeltsch, Albert. (2001). "Structure and function of type II restriction endonucleases". Nucleic Acids Research. 29 (18): 3705–3727. doi:10.1093/nar/29.18.3705. PMC 55916Freely accessible. PMID 11557805. 

Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081).

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Restriction endonuclease BglII Provide feedback

Members of this family are predominantly found in prokaryotic restriction endonuclease BglII, and adopt a structure consisting of an alpha/beta core containing a six-stranded beta-sheet surrounded by five alpha-helices, two of which are involved in homodimerisation of the endonuclease. They recognise the double-stranded DNA sequence AGATCT and cleave after A-1, resulting in specific double-stranded fragments with terminal 5'-phosphates [1].

Literature references

  1. Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK; , Nat Struct Biol. 2000;7:134-140.: Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution. PUBMED:10655616 EPMC:10655616

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015278

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 [PUBMED:15121719, PUBMED:12665693], as summarised below:

  • Type I enzymes (EC) 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) activities.
  • Type II enzymes (EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
  • Type III enzymes (EC) 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).
  • Type IV enzymes target methylated DNA.

Type II restriction endonucleases (EC) 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 [PUBMED:15770420]. However, there is still considerable diversity amongst restriction endonucleases [PUBMED:14576294, PUBMED: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 [PUBMED:11557805].

This entry represents BglII restriction endonucleases, which recognise AGATCT and cleaves after A-1 [PUBMED:10655616, PUBMED:11175900]. BglII adopts a structure consisting of an alpha/beta core containing a six-stranded beta-sheet surrounded by five alpha-helices, two of which are involved in homodimerisation of the endonuclease.

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Seed source: pdb_1dfm
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 9
Number in full: 70
Average length of the domain: 176.20 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 83.22 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 22.1 21.6
Noise cut-off 20.1 19.1
Model length: 166
Family (HMM) version: 9
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Endonuc-BglII domain has been found. There are 10 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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