1DMU

Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.

Newman, M.Lunnen, K.Wilson, G.Greci, J.Schildkraut, I.Phillips, S.E.

(1998) EMBO J 17: 5466-5476

  • DOI: 10.1093/emboj/17.18.5466
  • Primary Citation of Related Structures:  
    1DMU

  • PubMed Abstract: 
  • The crystal structure of the type II restriction endonuclease BglI bound to DNA containing its specific recognition sequence has been determined at 2.2 A resolution. This is the first structure of a restriction endonuclease that recognizes and cleaves an interrupted DNA sequence, producing 3' overhanging ends ...

    The crystal structure of the type II restriction endonuclease BglI bound to DNA containing its specific recognition sequence has been determined at 2.2 A resolution. This is the first structure of a restriction endonuclease that recognizes and cleaves an interrupted DNA sequence, producing 3' overhanging ends. BglI is a homodimer that binds its specific DNA sequence with the minor groove facing the protein. Parts of the enzyme reach into both the major and minor grooves to contact the edges of the bases within the recognition half-sites. The arrangement of active site residues is strikingly similar to other restriction endonucleases, but the co-ordination of two calcium ions at the active site gives new insight into the catalytic mechanism. Surprisingly, the core of a BglI subunit displays a striking similarity to subunits of EcoRV and PvuII, but the dimer structure is dramatically different. The BglI-DNA complex demonstrates, for the first time, that a conserved subunit fold can dimerize in more than one way, resulting in different DNA cleavage patterns.


    Related Citations: 
    • Method for producing the BglI restriction endonuclease and methylase
      Lunnen, K.D., Wilson, G.G.
      (1994) Patent --: --

    Organizational Affiliation

    School of Biochemistry and Molecular Biology, and North of England Structural Biology Centre, University of Leeds, Leeds LS2 9JT, UK.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BGLI RESTRICTION ENDONUCLEASEB [auth A]299Bacillus subtilisMutation(s): 0 
Gene Names: bglIR
EC: 3.1.21.4
UniProt
Find proteins for O68557 (Bacillus subtilis)
Explore O68557 
Go to UniProtKB:  O68557
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3')A [auth F]17N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    BME
    Query on BME

    Download Ideal Coordinates CCD File 
    G [auth A]BETA-MERCAPTOETHANOL
    C2 H6 O S
    DGVVWUTYPXICAM-UHFFFAOYSA-N
     Ligand Interaction
    CA
    Query on CA

    Download Ideal Coordinates CCD File 
    C [auth F], D [auth A], E [auth A], F [auth A]CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.239 
    • R-Value Work: 0.177 
    • R-Value Observed: 0.183 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 78.48α = 90
    b = 81.6β = 90
    c = 117.06γ = 90
    Software Package:
    Software NamePurpose
    SHARPphasing
    X-PLORrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1999-12-18
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2021-02-03
      Changes: Database references, Derived calculations