3BAM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 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.Mol.Biol. 5: 910-916

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

  • 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: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)
A, B
213Bacillus amyloliquefaciensGene Names: bamHIR
EC: 3.1.21.4
Find proteins for P23940 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P23940
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')C12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*G)-3')D4N/A
Entity ID: 3
MoleculeChainsLengthOrganism
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 SDF File 
Download CCD File 
A, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.400α = 90.00
b = 79.600β = 90.00
c = 67.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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