2VLA

Crystal structure of restriction endonuclease BpuJI recognition domain in complex with cognate DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

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This is version 1.3 of the entry. See complete history. 


Literature

The Recognition Domain of the Bpuji Restriction Endonuclease in Complex with Cognate DNA at 1.3-A Resolution.

Sukackaite, R., Grazulis, S., Bochtler, M., Siksnys, V.

(2008) J Mol Biol 378: 1084

  • DOI: 10.1016/j.jmb.2008.03.041
  • Primary Citation of Related Structures:  
    2VLA

  • PubMed Abstract: 

    • Type IIS restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. The restriction endonuclease BpuJI recognizes the asymmetric sequence 5'-CCCGT; however, it cuts at multiple sites in the vicinity of the target sequence ...

    Type IIS restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. The restriction endonuclease BpuJI recognizes the asymmetric sequence 5'-CCCGT; however, it cuts at multiple sites in the vicinity of the target sequence. BpuJI consists of two physically separate domains, with catalytic and dimerization functions in the C-terminal domain and DNA recognition functions in the N-terminal domain. Here we report the crystal structure of the BpuJI recognition domain bound to cognate DNA at 1.3-A resolution. This region folds into two winged-helix subdomains, D1 and D2, interspaced by the DL subdomain. The D1 and D2 subdomains of BpuJI share structural similarity with the similar subdomains of the FokI DNA-binding domain; however, their orientations in protein-DNA complexes are different. Recognition of the 5'-CCCGT target sequence is achieved by BpuJI through the major groove contacts of amino acid residues located on both the helix-turn-helix motifs and the N-terminal arm. The role of these interactions in DNA recognition is also corroborated by mutational analysis.

    Organizational Affiliation: 

    Institute of Biotechnology, Graiciuno 8, 02241 Vilnius, Lithuania.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RESTRICTION ENDONUCLEASE R.BPUJIA285Bacillus pumilusMutation(s): 0 
Gene Names: bpuJIR
EC: 3.1.21.4
Find proteins for A3FMN7 (Bacillus pumilus)
Explore A3FMN7 
Go to UniProtKB:  A3FMN7
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*TP*AP*CP*CP*CP*GP*TP*GP *GP*A)-3'B [auth L]12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP *CP*C)-3'C [auth M]12N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PG6
      Query on PG6
      Download Ideal Coordinates CCD File 
      		 D [auth A]1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
      C12 H26 O6
      DMDPGPKXQDIQQG-UHFFFAOYSA-N      		 Ligand Interaction
      NA
      Query on NA
      Download Ideal Coordinates CCD File 
      		 E [auth A]SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.30 Å
      • R-Value Free: 0.166 
      • R-Value Work: 0.138 
      • R-Value Observed: 0.140 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 56.292α = 90
      b = 167.513β = 90
      c = 43.846γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      MOSFLMdata reduction
      SCALAdata scaling
      MLPHAREphasing

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2008-05-06
        Type: Initial release
      • Version 1.1: 2011-05-08
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2019-07-24
        Changes: Data collection