3BAM

RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The role of metals in catalysis by the restriction endonuclease BamHI.

Viadiu, H.Aggarwal, A.K.

(1998) Nat Struct Biol 5: 910-916

  • DOI: 10.1038/2352
  • Primary Citation of Related Structures:  
    2BAM, 3BAM

  • PubMed Abstract: 
  • Type II restriction enzymes are characterized by their remarkable specificity and simplicity. They require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. However, most of the structural work on endonucleas ...

    Type II restriction enzymes are characterized by their remarkable specificity and simplicity. They require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. However, most of the structural work on endonucleases has been performed in the absence of metals, leaving unanswered questions about their mechanisms of DNA cleavage. Here we report structures of the endonuclease BamHI-DNA complex, determined in the presence of Mn2+ and Ca2+, that describe the enzyme at different stages of catalysis. Overall, the results support a two-metal mechanism of DNA cleavage for BamHI which is distinct from that of EcoRV.


    Related Citations: 
    • Structure of Bam Hi Endonuclease Bound to DNA: Partial Folding and Unfolding on DNA Binding
      Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I., Aggarwal, A.K.
      (1995) Science 269: 656

    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)AB213Bacillus amyloliquefaciensMutation(s): 0 
Gene Names: bamHIR
EC: 3.1.21.4
Find proteins for P23940 (Bacillus amyloliquefaciens)
Explore P23940 
Go to UniProtKB:  P23940
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')C12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*TP*G)-3')D4N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*AP*TP*CP*CP*AP*TP*A)-3')E8N/A
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        MN
        Query on MN

        Download CCD File 
        A, D
        MANGANESE (II) ION
        Mn
        WAEMQWOKJMHJLA-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.80 Å
        • R-Value Free: 0.268 
        • R-Value Work: 0.226 
        • R-Value Observed: 0.226 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 106.4α = 90
        b = 79.6β = 90
        c = 67.6γ = 90
        Software Package:
        Software NamePurpose
        X-PLORmodel building
        X-PLORrefinement
        DENZOdata reduction
        SCALEPACKdata scaling
        X-PLORphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 1999-01-13
          Type: Initial release
        • Version 1.1: 2007-10-16
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance