3HQF

Crystal structure of restriction endonuclease EcoRII N-terminal effector-binding domain in complex with cognate DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.

Golovenko, D.Manakova, E.Tamulaitiene, G.Grazulis, S.Siksnys, V.

(2009) Nucleic Acids Res 37: 6613-6624

  • DOI: 10.1093/nar/gkp699
  • Primary Citation of Related Structures:  
    3HQF, 3HQG

  • PubMed Abstract: 
  • EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T); however, it shows no activity on a single recognition site. To activate cleavage it requires binding of an additional target site as an allosteric effector. EcoRII dimer consists of three structural units: a central catalytic core, made from two copies of the C-terminal domain (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N) ...

    EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T); however, it shows no activity on a single recognition site. To activate cleavage it requires binding of an additional target site as an allosteric effector. EcoRII dimer consists of three structural units: a central catalytic core, made from two copies of the C-terminal domain (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N). Here, we report DNA-bound EcoRII-N and EcoRII-C structures, which show that EcoRII combines two radically different structural mechanisms to interact with the effector and substrate DNA. The catalytic EcoRII-C dimer flips out the central T:A base pair and makes symmetric interactions with the CC:GG half-sites. The EcoRII-N effector domain monomer binds to the target site asymmetrically in a single defined orientation which is determined by specific hydrogen bonding and van der Waals interactions with the central T:A pair in the major groove. The EcoRII-N mode of the target site recognition is shared by the large class of higher plant transcription factors of the B3 superfamily.


    Related Citations: 
    • Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold
      Zhou, X.E., Wang, Y., Reuter, M., Mucke, M., Kruger, D.H., Meehan, E.J., Chen, L.
      (2004) J Mol Biol 335: 307

    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Restriction endonucleaseA181Escherichia coliMutation(s): 0 
Gene Names: 
EC: 3.1.21.4
UniProt
Find proteins for O69414 (Escherichia coli)
Explore O69414 
Go to UniProtKB:  O69414
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*CP*CP*TP*GP*GP*CP*G)-3'B9N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*GP*CP*CP*AP*GP*GP*GP*C)-3'C9N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.51 Å
      • R-Value Free: 0.229 
      • R-Value Work: 0.187 
      • R-Value Observed: 0.191 
      • Space Group: P 43 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 43.156α = 90
      b = 43.156β = 90
      c = 253.648γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      AMoREphasing
      MOSFLMdata reduction
      SCALAdata scaling
      PDB_EXTRACTdata extraction

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2009-09-22
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Advisory, Refinement description, Version format compliance