1M08

Crystal structure of the unbound nuclease domain of ColE7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

The Crystal Structure of the Nuclease Domain of Colicin E7 Suggests a Mechanism for Binding to Double-stranded DNA by the H-N-H Endonucleases

Cheng, Y.S.Hsia, K.C.Doudeva, L.G.Chak, K.F.Yuan, H.S.

(2002) J Mol Biol 324: 227-236

  • DOI: https://doi.org/10.1016/s0022-2836(02)01092-6
  • Primary Citation of Related Structures:  
    1M08

  • PubMed Abstract: 

    The bacterial toxin ColE7 contains an H-N-H endonuclease domain (nuclease ColE7) that digests cellular DNA or RNA non-specifically in target cells, leading to cell death. In the host cell, protein Im7 forms a complex with ColE7 to inhibit its nuclease activity. Here, we present the crystal structure of the unbound nuclease ColE7 at a resolution of 2.1A. Structural comparison between the unbound and bound nuclease ColE7 in complex with Im7, suggests that Im7 is not an allosteric inhibitor that induces backbone conformational changes in nuclease ColE7, but rather one that inhibits by blocking the substrate-binding site. There were two nuclease ColE7 molecules in the P1 unit cell in crystals and they appeared as a dimer related to each other by a non-crystallographic dyad symmetry. Gel-filtration and cross-linking experiments confirmed that nuclease ColE7 indeed formed dimers in solution and that the dimeric conformation was more favored in the presence of double-stranded DNA. Structural comparison of nuclease ColE7 with the His-Cys box homing endonuclease I-PpoI further demonstrated that H-N-H motifs in dimeric nuclease ColE7 were oriented in a manner very similar to that of the betabetaalpha-fold of the active sites found in dimeric I-PpoI. A mechanism for the binding of double-stranded DNA by dimeric H-N-H nuclease ColE7 is suggested.


  • Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROC.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Colicin E7
A, B
131Escherichia coli str. K-12 substr. W3110Mutation(s): 0 
Gene Names: COLE7 or CEA
EC: 3.1
UniProt
Find proteins for Q47112 (Escherichia coli)
Explore Q47112 
Go to UniProtKB:  Q47112
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47112
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.7α = 96.8
b = 39.2β = 103.9
c = 53.2γ = 91.4
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-08
    Changes: Data collection, Refinement description