1BGB

ECORV ENDONUCLEASE COMPLEX WITH 5'-CGGGATATCCC DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.

Horton, N.C.Perona, J.J.

(1998) J Biol Chem 273: 21721-21729

  • DOI: 10.1074/jbc.273.34.21721
  • Primary Citation of Related Structures:  
    1BGB

  • PubMed Abstract: 
  • The 2.1-A cocrystal structure of EcoRV endonuclease bound to 5'-CGGGATATCCC, in a crystal lattice isomorphous with the cocrystallized undecamer 5'-AAAGATATCTT previously determined, shows novel base recognition in the major groove of the DNA flanking the GATATC target site ...

    The 2.1-A cocrystal structure of EcoRV endonuclease bound to 5'-CGGGATATCCC, in a crystal lattice isomorphous with the cocrystallized undecamer 5'-AAAGATATCTT previously determined, shows novel base recognition in the major groove of the DNA flanking the GATATC target site. Lys104 of the enzyme interacts through water molecules with the exocyclic N-4 amino groups of flanking cytosines. Steric exclusion of water molecule-binding sites by the 5-methyl group of thymine drives the adoption of alternative water-mediated contacts with AT versus GC flanks. This structure provides a rare example of structural adaptability in the recognition of different DNA sequences by a protein and suggests preferred strategies for the expansion of target site specificity by EcoRV.


    Related Citations: 
    • Role of Protein-Induced Bending in the Specificity of DNA Recognition-Crystal Structure of EcoRV Endonuclease Complexed with D(Aaagat) + D(Atctt)
      Horton, N.C., Perona, J.J.
      (1998) J Mol Biol 277: 779
    • Conformational Transitions and Structural Deformability of EcoRV Endonuclease Revealed by Crystallographic Analysis
      Perona, J.J., Martin, A.M.
      (1997) J Mol Biol 273: 207

    Organizational Affiliation

    Department of Chemistry and Interdepartmental Program in Biochemistry and Molecular Biology, University of California, Santa Barbara, California 93106-9510, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ECORV ENDONUCLEASEC [auth A], D [auth B]244Escherichia coliMutation(s): 0 
Gene Names: ecoRVR
EC: 3.1.21.4
UniProt
Find proteins for P04390 (Escherichia coli)
Explore P04390 
Go to UniProtKB:  P04390
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')A [auth C], B [auth D]11N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.246 
    • R-Value Work: 0.184 
    • R-Value Observed: 0.184 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 49.4α = 96
    b = 50.2β = 109
    c = 64.1γ = 108
    Software Package:
    Software NamePurpose
    X-PLORmodel building
    X-PLORrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    X-PLORphasing

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1998-10-28
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance