4ZSF

Crystal structure of pre-specific restriction endonuclease BsaWI-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI.

Tamulaitis, G.Rutkauskas, M.Zaremba, M.Grazulis, S.Tamulaitiene, G.Siksnys, V.

(2015) Nucleic Acids Res. 43: 8100-8110

  • DOI: 10.1093/nar/gkv768

  • PubMed Abstract: 
  • Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W/CCGGW-3' (W stands for A or T, '/' denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their ta ...

    Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W/CCGGW-3' (W stands for A or T, '/' denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their target sites. These enzymes are arranged as dimers or tetramers, and require binding of one, two or three DNA targets for their optimal catalytic activity. Here, we present a crystal structure and biochemical characterization of the restriction endonuclease BsaWI. BsaWI is arranged as an 'open' configuration dimer and binds a single DNA copy through a minor groove contacts. In the crystal primary BsaWI dimers form an indefinite linear chain via the C-terminal domain contacts implying possible higher order aggregates. We show that in solution BsaWI protein exists in a dimer-tetramer-oligomer equilibrium, but in the presence of specific DNA forms a tetramer bound to two target sites. Site-directed mutagenesis and kinetic experiments show that BsaWI is active as a tetramer and requires two target sites for optimal activity. We propose BsaWI mechanism that shares common features both with dimeric Ecl18kI/SgrAI and bona fide tetrameric NgoMIV/SfiI enzymes.


    Organizational Affiliation

    Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BsaWI endonuclease
A
272Geobacillus stearothermophilusMutation(s): 0 
Gene Names: bsaWIR
Find proteins for Q6UQ65 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q6UQ65
Entity ID: 2
MoleculeChainsLengthOrganism
DNAB14synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN

Download SDF File 
Download CCD File 
A
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 89.562α = 90.00
b = 136.336β = 90.00
c = 73.482γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MAR345dtbdata collection
SHELXphasing
Cootmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of LithuaniaLithuaniaMIP-41/2013

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release