2ODH

Restriction Endonuclease BCNI in the Absence of DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 1
MoleculeChainsSequence LengthOrganismDetails
R.BcnI
A
238Brevibacillus centrosporusMutation(s): 0 
Gene Names: bcnIR
Find proteins for Q8RNV8 (Brevibacillus centrosporus)
Go to UniProtKB:  Q8RNV8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.176α = 90.00
b = 68.176β = 90.00
c = 127.207γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SHARPphasing
DMphasing
SHELXDphasing
MLPHAREphasing
MOSFLMdata reduction
NCSREFmodel building
REFMACrefinement
ARP/wARPmodel building
CCP4data scaling

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
  • Version 1.4: 2018-01-24
    Type: Structure summary