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: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.177 

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This is version 1.2 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

  • 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 cleave ...

    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: US 536682, New England Biolabs, Beverly, MA --: --


    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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BGLI RESTRICTION ENDONUCLEASE
A
299Bacillus subtilisMutation(s): 0 
Gene Names: bglIR
EC: 3.1.21.4
Find proteins for O68557 (Bacillus subtilis)
Go to UniProtKB:  O68557
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3')F17N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.177 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 78.480α = 90.00
b = 81.600β = 90.00
c = 117.060γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHARPphasing
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance