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 
  • R-Value Observed: 0.175 

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:  
    2ODH, 2ODI, 2Q10

  • 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 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 ...

    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

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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
R.BcnIE [auth A],
F [auth B]		238Brevibacillus centrosporusMutation(s): 6 
Gene Names: bcnIR
UniProt
Find proteins for Q8RNV8 (Brevibacillus centrosporus)
Explore Q8RNV8 
Go to UniProtKB:  Q8RNV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RNV8
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'A [auth C],
C [auth E]		11N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'B [auth D],
D [auth F]		11N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		E [auth A],
F [auth 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 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.553α = 90
b = 87.87β = 90
c = 79.391γ = 90
Software Package:
Software NamePurpose
SHELXDphasing
SHARPphasing
NCSREFmodel building
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
SHELXEmodel building
ARP/wARPmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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