1BGB

ECORV ENDONUCLEASE COMPLEX WITH 5'-CGGGATATCCC DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 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


  • 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 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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ECORV ENDONUCLEASE
A, B
244Escherichia coliGene Names: ecoRVR
EC: 3.1.21.4
Find proteins for P04390 (Escherichia coli)
Go to UniProtKB:  P04390
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')C,D11N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.400α = 96.00
b = 50.200β = 109.00
c = 64.100γ = 108.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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