2EWF

Crystal structure of the site-specific DNA nickase N.BspD6I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit.

Kachalova, G.S.Rogulin, E.A.Yunusova, A.K.Artyukh, R.I.Perevyazova, T.A.Matvienko, N.I.Zheleznaya, L.A.Bartunik, H.D.

(2008) J.Mol.Biol. 384: 489-502

  • DOI: 10.1016/j.jmb.2008.09.033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The heterodimeric restriction endonuclease R.BspD6I from Bacillus species D6 recognizes a pseudosymmetric sequence and cuts both DNA strands outside the recognition sequence. The large subunit, Nt.BspD6I, acts as a type IIS site-specific monomeric ni ...

    The heterodimeric restriction endonuclease R.BspD6I from Bacillus species D6 recognizes a pseudosymmetric sequence and cuts both DNA strands outside the recognition sequence. The large subunit, Nt.BspD6I, acts as a type IIS site-specific monomeric nicking endonuclease. The isolated small subunit, ss.BspD6I, does not bind DNA and is not catalytically active. We solved the crystal structures of Nt.BspD6I and ss.BspD6I at high resolution. Nt.BspD6I consists of three domains, two of which exhibit structural similarity to the recognition and cleavage domains of FokI. ss.BspD6I has a fold similar to that of the cleavage domain of Nt.BspD6I, each containing a PD-(D/E)XK motif and a histidine as an additional putative catalytic residue. In contrast to the DNA-bound FokI structure, in which the cleavage domain is rotated away from the DNA, the crystal structure of Nt.BspD6I shows the recognition and cleavage domains in favorable orientations for interactions with DNA. Docking models of complexes of Nt.BspD6I and R.BspD6I with cognate DNA were constructed on the basis of structural similarity to individual domains of FokI, R.BpuJI and HindIII. A three-helix bundle forming an interdomain linker in Nt.BspD6I acts as a rigid spacer adjusting the orientations of the spatially separated domains to match the distance between the recognition and cleavage sites accurately.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of the site-specific DNA nickase Nb.BspD6I
      Kachalova, G.S.,Rogulin, E.A.,Artyukh, R.I.,Perevyazova, T.A.,Zheleznaya, L.A.,Matvienko, N.I.,Bartunik, H.D.
      (2005) Acta Crystallogr.,Sect.F 61: 332
    • Cloning and sequencing of the gene of site-specific nickase N.BspD6I
      Perevyazova, T.A.,Rogulin, E.A.,Zheleznaya, L.A.,Matvienko, N.I.
      (2003) Biochemistry Mosc. 68: 984


    Organizational Affiliation

    Max Planck Unit for Structural Molecular Biology, MPG-ASMB c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicking endonuclease N.BspD6I
A
610Bacillus sp. D6Mutation(s): 0 
Gene Names: bspD6R1
Find proteins for A3FEV7 (Bacillus sp. D6)
Go to UniProtKB:  A3FEV7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.553α = 90.00
b = 92.562β = 111.88
c = 76.349γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement
SHELXmodel building
SHELXSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance