2JBG

crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Conserved Asparagine in the Hnh Motif Serves an Important Structural Role in Metal Finger Endonucleases.

Huang, H.Yuan, H.S.

(2007) J.Mol.Biol. 368: 812

  • DOI: 10.1016/j.jmb.2007.02.044
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The HNH motif is a small nucleic acid binding and cleavage module, widespread in metal finger endonucleases in all life kingdoms. Here we studied a non-specific endonuclease, the nuclease domain of ColE7 (N-ColE7), to decipher the role of the conserv ...

    The HNH motif is a small nucleic acid binding and cleavage module, widespread in metal finger endonucleases in all life kingdoms. Here we studied a non-specific endonuclease, the nuclease domain of ColE7 (N-ColE7), to decipher the role of the conserved asparagine and histidine residues in the HNH motif. We found, using fluorescence resonance energy transfer (FRET) assays, that the DNA hydrolysis activity of H545 N-ColE7 mutants was completely abolished while activities of N560 and H573 mutants varied from 6.9% to 83.2% of the wild-type activity. The crystal structures of three N-ColE7 mutants in complex with the inhibitor Im7, N560A-Im7, N560D-Im7 and H573A-Im7, were determined at a resolution of 1.9 A to 2.2 A. H573 is responsible for metal ion binding in the wild-type protein, as the zinc ion is still partially associated in the structure of H573A, suggesting that H573 plays a supportive role in metal binding. Both N560A and N560D contain a disordered loop in the HNH motif due to the disruption of the hydrogen bond network surrounding the side-chain of residue 560, and as a result, the imidazole ring of the general base residue H545 is tilted slightly and the scissile phosphate is shifted, leading to the large reductions in hydrolysis activities. These results suggest that the highly conserved asparagine in the HNH motif, in general, plays a structural role in constraining the loop in the metal finger structure and keeping the general base histidine and scissile phosphate in the correct position for DNA hydrolysis.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COLICIN-E7 IMMUNITY PROTEIN
A, C
87Escherichia coliMutation(s): 0 
Gene Names: imm (ceiE7)
Find proteins for Q03708 (Escherichia coli)
Go to UniProtKB:  Q03708
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COLICIN E7
B, D
131Escherichia coliMutation(s): 1 
Gene Names: colE7 (cea)
EC: 3.1.-.-
Find proteins for Q47112 (Escherichia coli)
Go to UniProtKB:  Q47112
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 119.180α = 90.00
b = 62.683β = 90.00
c = 74.785γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-12-07 
  • Released Date: 2007-04-03 
  • Deposition Author(s): Huang, H., Yuan, H.S.

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Data collection