PDBsum entry 1es8

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Hydrolase PDB id
Protein chain
197 a.a.
Waters ×81
PDB id:
Name: Hydrolase
Title: Crystal structure of free bglii
Structure: Restriction endonuclease bglii. Chain: a. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562
2.30Å     R-factor:   0.214     R-free:   0.258
Authors: C.M.Lukacs,A.K.Aggarwal
Key ref:
C.M.Lukacs et al. (2001). Structure of free BglII reveals an unprecedented scissor-like motion for opening an endonuclease. Nat Struct Biol, 8, 126-130. PubMed id: 11175900 DOI: 10.1038/84111
07-Apr-00     Release date:   17-Jan-01    
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Protein chain
Pfam   ArchSchema ?
Q45488  (T2B2_BACIU) -  Type-2 restriction enzyme BglII
223 a.a.
197 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Type Ii site-specific deoxyribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
      Cofactor: Magnesium
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     hydrolase activity     7 terms  


DOI no: 10.1038/84111 Nat Struct Biol 8:126-130 (2001)
PubMed id: 11175900  
Structure of free BglII reveals an unprecedented scissor-like motion for opening an endonuclease.
C.M.Lukacs, R.Kucera, I.Schildkraut, A.K.Aggarwal.
Restriction endonuclease BglII completely encircles its target DNA, making contacts to both the major and minor grooves. To allow the DNA to enter and leave the binding cleft, the enzyme dimer has to rearrange. To understand how this occurs, we have solved the structure of the free enzyme at 2.3 A resolution, as a complement to our earlier work on the BglII-DNA complex. Unexpectedly, the enzyme opens by a dramatic 'scissor-like' motion, accompanied by a complete rearrangement of the alpha-helices at the dimer interface. Moreover, within each monomer, a set of residues--a 'lever'--lowers or raises to alternately sequester or expose the active site residues. Such an extreme difference in free versus complexed structures has not been reported for other restriction endonucleases. This elegant mechanism for capturing DNA may extend to other enzymes that encircle DNA.
  Selected figure(s)  
Figure 2.
Figure 2. Comparison of free and DNA bound monomers to show the lever motion. a, The lever segment (magenta) and helix 4 (blue) undergo the largest local conformational change. The lever projects downward in the free enzyme (left) but upward in the complex (right). The length of helix 4 also change in going from free to the complexed state. b, A close up of the active site residues. In the free enzyme (left), the catalytic residues Asn 69, Asp 84, Glu 93 and Gln 95 are sequestered by extensive intramolecular hydrogen bonds with residues Asn 105 and Arg 108 from helix 4. Shown also is the position of a putative acetate ion. In the complex (right), several of these hydrogen bonds are broken, and residues reorient to form the active site. Shown also as a ball-stick tetrahedron is the position of the scissile phosphate group in the complex.
Figure 3.
Figure 3. A view of the scissor-like motion. The complex (right) is shown with the DNA aligned horizontally. The two protein monomers are colored blue and purple, respectively. The free enzyme (left) is shown with a DNA modeled between the two monomers. The two monomers move symmetrically in opposite directions along the DNA axis.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 126-130) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19364803 A.Doi, S.P.Pack, T.Kodaki, and K.Makino (2009).
Reinvestigation of the molecular influence of hypoxanthine on the DNA cleavage efficiency of restriction endonucleases BglII, EcoRI and BamHI.
  J Biochem, 146, 201-208.  
19533711 D.D.Young, J.M.Govan, M.O.Lively, and A.Deiters (2009).
Photochemical regulation of restriction endonuclease activity.
  Chembiochem, 10, 1612-1616.  
15893669 S.A.Townson, J.C.Samuelson, S.Y.Xu, and A.K.Aggarwal (2005).
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
  Structure, 13, 791-801.
PDB codes: 1vrr 1yuv
12142452 M.Fuxreiter, and I.Simon (2002).
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
  Protein Sci, 11, 1978-1983.  
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.