1D2I

CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BGLII COMPLEXED WITH DNA 16-MER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution.

Lukacs, C.M.Kucera, R.Schildkraut, I.Aggarwal, A.K.

(2000) Nat.Struct.Mol.Biol. 7: 134-140

  • DOI: 10.1038/72405
  • Primary Citation of Related Structures:  1DFM

  • PubMed Abstract: 
  • Restriction endonucleases are remarkably resilient to alterations in their DNA binding specificity. To understand the basis of this immutability, we have determined the crystal structure of endonuclease BglII bound to its recognition sequence (AGATCT ...

    Restriction endonucleases are remarkably resilient to alterations in their DNA binding specificity. To understand the basis of this immutability, we have determined the crystal structure of endonuclease BglII bound to its recognition sequence (AGATCT), at 1. 5 A resolution. We compare the structure of BglII to endonuclease BamHI, which recognizes a closely related DNA site (GGATCC). We show that both enzymes share a similar alpha/beta core, but in BglII, the core is augmented by a beta-sandwich domain that encircles the DNA to provide extra specificity. Remarkably, the DNA is contorted differently in the two structures, leading to different protein-DNA contacts for even the common base pairs. Furthermore, the BglII active site contains a glutamine in place of the glutamate at the general base position in BamHI, and only a single metal is found coordinated to the putative nucleophilic water and the phosphate oxygens. This surprising diversity in structures shows that different strategies can be successful in achieving site-specific recognition and catalysis in restriction endonucleases.


    Organizational Affiliation

    Structural Biology Program, Department of Physiology and Biophysics, Mt. Sinai School of Medicine, 1425 Madison Avenue, New York, New York 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RESTRICTION ENDONUCLEASE BGLII)
A, B
223Bacillus subtilisGene Names: bglIIR
EC: 3.1.21.4
Find proteins for Q45488 (Bacillus subtilis)
Go to UniProtKB:  Q45488
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3')C,D16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.800α = 90.00
b = 101.700β = 90.00
c = 116.900γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHARPphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance