1ESG

RESTRICTION ENDONUCLEASE BAMHI BOUND TO A NON-SPECIFIC DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of BamHI bound to nonspecific DNA: a model for DNA sliding.

Viadiu, H.Aggarwal, A.K.

(2000) Mol.Cell 5: 889-895


  • PubMed Abstract: 
  • The central problem faced by DNA binding proteins is how to select the correct DNA sequence from the sea of nonspecific sequences in a cell. The problem is particularly acute for bacterial restriction enzymes because cleavage at an incorrect DNA site ...

    The central problem faced by DNA binding proteins is how to select the correct DNA sequence from the sea of nonspecific sequences in a cell. The problem is particularly acute for bacterial restriction enzymes because cleavage at an incorrect DNA site could be lethal. To understand the basis of this selectivity, we report here the crystal structure of endonuclease BamHI bound to noncognate DNA. We show that, despite only a single base pair change in the recognition sequence, the enzyme adopts an open configuration that is on the pathway between free and specifically bound forms of the enzyme. Surprisingly, the DNA drops out of the binding cleft with a total loss of base-specific and backbone contacts. Taken together, the structure provides a remarkable snapshot of an enzyme poised for linear diffusion (rather than cleavage) along the DNA.


    Related Citations: 
    • A step towards understanding protein-DNA specificity: crystallization of the restriction endonuclease BamHI with a non-specific DNA
      Viadiu, H.,Kucera, R.,Schildkraut, I.,Aggarwal, A.K.
      (2000) TO BE PUBLISHED --: --


    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: 3
MoleculeChainsSequence LengthOrganismDetails
TYPE II RESTRICTION ENZYME BAMHI
A, B
213Bacillus amyloliquefaciensMutation(s): 0 
Gene 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*GP*GP*AP*TP*TP*CP*A)-3')C8N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*AP*AP*TP*CP*CP*A)-3')D8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 114.800α = 90.00
b = 91.100β = 90.00
c = 66.400γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation