1MZ8

CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND A ZINC ION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Metal ions and phosphate binding in the H-N-H motif: crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions

Sui, M.J.Tsai, L.C.Hsia, K.C.Doudeva, L.G.Ku, W.Y.Han, G.W.Yuan, H.S.

(2002) PROTEIN SCI. 11: 2947-2957

  • DOI: 10.1110/ps.0220602

  • PubMed Abstract: 
  • H-N-H is a motif found in the nuclease domain of a subfamily of bacteria toxins, including colicin E7, that are capable of cleaving DNA nonspecifically. This H-N-H motif has also been identified in a subfamily of homing endonucleases, which cleave DN ...

    H-N-H is a motif found in the nuclease domain of a subfamily of bacteria toxins, including colicin E7, that are capable of cleaving DNA nonspecifically. This H-N-H motif has also been identified in a subfamily of homing endonucleases, which cleave DNA site specifically. To better understand the role of metal ions in the H-N-H motif during DNA hydrolysis, we crystallized the nuclease domain of colicin E7 (nuclease-ColE7) in complex with its inhibitor Im7 in two different crystal forms, and we resolved the structures of EDTA-treated, Zn(2+)-bound and Mn(2+)-bound complexes in the presence of phosphate ions at resolutions of 2.6 A to 2.0 A. This study offers the first determination of the structure of a metal-free and substrate-free enzyme in the H-N-H family. The H-N-H motif contains two antiparallel beta-strands linked to a C-terminal alpha-helix, with a divalent metal ion located in the center. Here we show that the metal-binding sites in the center of the H-N-H motif, for the EDTA-treated and Mg(2+)-soaked complex crystals, were occupied by water molecules, indicating that an alkaline earth metal ion does not reside in the same position as a transition metal ion in the H-N-H motif. However, a Zn(2+) or Mn(2+) ions were observed in the center of the H-N-H motif in cases of Zn(2+) or Mn(2+)-soaked crystals, as confirmed in anomalous difference maps. A phosphate ion was found to bridge between the divalent transition metal ion and His545. Based on these structures and structural comparisons with other nucleases, we suggest a functional role for the divalent transition metal ion in the H-N-H motif in stabilizing the phosphoanion in the transition state during hydrolysis.


    Organizational Affiliation

    Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan 11472, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Colicin E7 immunity protein
A, C
87Escherichia coliGene Names: imm (ceiE7)
Find proteins for Q03708 (Escherichia coli)
Go to UniProtKB:  Q03708
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Colicin E7
B, D
131Escherichia coliGene 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
PO4
Query on PO4

Download SDF File 
Download CCD File 
B, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 119.735α = 90.00
b = 62.410β = 90.00
c = 74.137γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description