2ODI

Restriction Endonuclease BCNI-Cognate DNA Substrate Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA.

Sokolowska, M.Kaus-Drobek, M.Czapinska, H.Tamulaitis, G.Szczepanowski, R.H.Urbanke, C.Siksnys, V.Bochtler, M.

(2007) J.Mol.Biol. 369: 722-734

  • DOI: 10.1016/j.jmb.2007.03.018
  • Primary Citation of Related Structures:  
  • Also Cited By: 3IMB

  • PubMed Abstract: 
  • Restriction endonuclease BcnI cleaves duplex DNA containing the sequence CC/SGG (S stands for C or G, / designates a cleavage position) to generate staggered products with single nucleotide 5'-overhangs. Here, we show that BcnI functions as a monomer ...

    Restriction endonuclease BcnI cleaves duplex DNA containing the sequence CC/SGG (S stands for C or G, / designates a cleavage position) to generate staggered products with single nucleotide 5'-overhangs. Here, we show that BcnI functions as a monomer that interacts with its target DNA in 1:1 molar ratio and report crystal structures of BcnI in the absence and in the presence of DNA. In the complex with DNA, BcnI makes specific contacts with all five bases of the target sequence and not just with a half-site, as the protomer of a typical dimeric restriction endonuclease. Our data are inconsistent with BcnI dimerization and suggest that the enzyme introduces double-strand breaks by sequentially nicking individual DNA strands, although this remains to be confirmed by kinetic experiments. BcnI is remotely similar to the DNA repair protein MutH and shares approximately 20% sequence identity with the restriction endonuclease MvaI, which is specific for the related sequence CC/WGG (W stands for A or T). As expected, BcnI is structurally similar to MvaI and recognizes conserved bases in the target sequence similarly but not identically. BcnI has a unique machinery for the recognition of the central base-pair.


    Related Citations: 
    • Structural and Mechanistic Similarities between Restriction Endonucleases BcnI and MvaI and the DNA Repair Protein MutH.
      Sokolowska, M.,Kaus-Drobek, M.,Czapinska, H.,Tamulaitis, G.,Siksnys, V.,Bochtler, M.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    International Institute of Molecular and Cell Biology, Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
R.BcnI
A, B
238Brevibacillus centrosporusMutation(s): 0 
Gene Names: bcnIR
Find proteins for Q8RNV8 (Brevibacillus centrosporus)
Go to UniProtKB:  Q8RNV8
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'C,E11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'D,F11N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-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: 1.45 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.553α = 90.00
b = 87.870β = 90.00
c = 79.391γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SHELXDphasing
SHELXEmodel building
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SHARPphasing
NCSREFmodel building
ARP/wARPmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Advisory, Refinement description