1PT3

Crystal structures of nuclease-ColE7 complexed with octamer DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA binding and degradation by the HNH protein ColE7.

Hsia, K.C.Chak, K.F.Liang, P.H.Cheng, Y.S.Ku, W.Y.Yuan, H.S.

(2004) STRUCTURE 12: 205-214

  • DOI: 10.1016/j.str.2004.01.004

  • PubMed Abstract: 
  • The bacterial toxin ColE7 bears an HNH motif which has been identified in hundreds of prokaryotic and eukaryotic endonucleases, involved in DNA homing, restriction, repair, or chromosome degradation. The crystal structure of the nuclease domain of Co ...

    The bacterial toxin ColE7 bears an HNH motif which has been identified in hundreds of prokaryotic and eukaryotic endonucleases, involved in DNA homing, restriction, repair, or chromosome degradation. The crystal structure of the nuclease domain of ColE7 in complex with a duplex DNA has been determined at 2.5 A resolution. The HNH motif is bound at the minor groove primarily to DNA phosphate groups at and beyond the 3' side of the scissile phosphate, with little interaction with ribose groups and bases. This result provides a structural basis for sugar- and sequence-independent DNA recognition and the inhibition mechanism by inhibitor Im7, which blocks the substrate binding site but not the active site. Structural comparison shows that two families of endonucleases bind and bend DNA in a similar way to that of the HNH ColE7, indicating that endonucleases containing a "betabetaalpha-metal" fold of active site possess a universal mode for protein-DNA interactions.


    Organizational Affiliation

    Institute of Molecular Biology, National Yang-Ming University, Taipei, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Colicin E7
A, B
128Escherichia coliGene Names: colE7 (cea)
EC: 3.1.-.-
Find proteins for Q47112 (Escherichia coli)
Go to UniProtKB:  Q47112
Entity ID: 1
MoleculeChainsLengthOrganism
5'-GCGATCGC-3'C,D,G,H,E,F8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.430α = 90.00
b = 46.470β = 90.39
c = 78.450γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance