Crystal structure of small subunit (R.BspD6I2) of the heterodimeric restriction endonuclease R.BspD6I

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1016/j.jmb.2008.09.033
  • Primary Citation of Related Structures:  
    2EWF, 2P14

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heterodimeric restriction endonuclease R.BspD6I small subunit192Bacillus sp. D6Mutation(s): 0 
Gene Names: bspD6IR2
Find proteins for A3FEV8 (Bacillus sp. D6)
Explore A3FEV8 
Go to UniProtKB:  A3FEV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3FEV8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.429α = 90
b = 38.36β = 101.47
c = 61.995γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Bestdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description