1V15

CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases

Mate, M.J., Kleanthous, C.

(2004) J Biol Chem 279: 34763

  • DOI: 10.1074/jbc.M403719200
  • Primary Citation of Related Structures:  
    1V13, 1V14, 1V15

  • PubMed Abstract: 

    • Controversy surrounds the metal-dependent mechanism of H-N-H endonucleases, enzymes involved in a variety of biological functions, including intron homing and DNA repair. To address this issue we determined the crystal structures for complexes of the H-N-H motif containing bacterial toxin colicin E9 with Zn(2+), Zn(2+) ...

    Controversy surrounds the metal-dependent mechanism of H-N-H endonucleases, enzymes involved in a variety of biological functions, including intron homing and DNA repair. To address this issue we determined the crystal structures for complexes of the H-N-H motif containing bacterial toxin colicin E9 with Zn(2+), Zn(2+).DNA, and Mg(2+).DNA. The structures show that the rigid V-shaped architecture of the active site does not undergo any major conformational changes on binding to the minor groove of DNA and that the same interactions are made to the nucleic acid regardless of which metal ion is bound to the enzyme. The scissile phosphate contacts the single metal ion of the motif through distortion of the DNA brought about by the insertion of the Arg-96-Glu-100 salt bridge into the minor groove and a network of contacts to the DNA phosphate backbone that straddle the metal site. The Mg(2+)-bound structure reveals an unusual coordination scheme involving two H-N-H histidine residues, His-102 and His-127. The mechanism of DNA cleavage is likely related to that of other single metal ion-dependent endonucleases, such as I-PpoI and Vvn, although in these enzymes the single alkaline earth metal ion is coordinated by oxygen-bearing amino acids. The structures also provide a rationale as to why H-N-H endonucleases are inactive in the presence of Zn(2+) but active with other transition metal ions such as Ni(2+). This is because of coordination of the Zn(2+) ion through a third histidine, His-131. "Active" transition metal ions are those that bind more weakly to the H-N-H motif because of the disengagement of His-131, which we suggest allows a water molecule to complete the catalytic cycle.

    Related Citations: 
    • Specificity in Protein-Protein Interactions: The Structural Basis for Dual Recognition in Endonuclease Colicin-Immunity Protein Complexes
      Kuhlmann, U.C., Pommer, A.J., Moore, G.M., James, R., Kleanthous, C.
      (2000) J Mol Biol 301: 1163
    Organizational Affiliation: 

    Department of Biology, Area 10, P. O. Box 373, University of York, Heslington YO10 5YW, United Kingdom.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COLICIN E9A, B, C, D134Escherichia coliMutation(s): 1 
Gene Names: col, cei
EC: 3.1.21.1 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P09883 (Escherichia coli)
Explore P09883 
Go to UniProtKB:  P09883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09883
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
E, F, G, H, I, J, K, L
E, F, G, H, I, J, K, L
8N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.246 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.145α = 90
b = 123.31β = 90
c = 110.531γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance