1znv
How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor
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OverviewOverview
The nuclease domain of ColE7 (N-ColE7) contains an H-N-H motif that folds, in a beta beta alpha-metal topology. Here we report the crystal structures, of a Zn2+-bound N-ColE7 (H545E mutant) in complex with a 12-bp duplex DNA, and a Ni2+-bound N-ColE7 in complex with the inhibitor Im7 at a resolution, of 2.5 A and 2.0 A, respectively. Metal-dependent cleavage assays showed, that N-ColE7 cleaves double-stranded DNA with a single metal ion cofactor, Ni2+, Mg2+, Mn2+, and Zn2+. ColE7 purified from Escherichia coli contains, an endogenous zinc ion that was not replaced by Mg2+ at concentrations of, <25 mM, indicating that zinc is the physiologically relevant metal ion in, N-ColE7 in host E. coli. In the crystal structure of N-ColE7/DNA complex, the zinc ion is directly coordinated to three histidines and the DNA, scissile phosphate in a tetrahedral geometry. In contrast, Ni2+ is bound, in N-ColE7 in two different modes, to four ligands (three histidines and, one phosphate ion), or to five ligands with an additional water molecule., These data suggest that the divalent metal ion in the His-metal finger, motif can be coordinated to six ligands, such as Mg2+ in I-PpoI, Serratia, nuclease and Vvn, five ligands or four ligands, such as Ni2+ or Zn2+ in, ColE7. Universally, the metal ion in the His-metal finger motif is bound, to the DNA scissile phosphate and serves three roles during hydrolysis:, polarization of the P-O bond for nucleophilic attack, stabilization of the, phosphoanion transition state and stabilization of the cleaved product.
About this StructureAbout this Structure
1ZNV is a Protein complex structure of sequences from Escherichia coli with NI and PO4 as ligands. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+., Doudeva LG, Huang H, Hsia KC, Shi Z, Li CL, Shen Y, Cheng YS, Yuan HS, Protein Sci. 2006 Feb;15(2):269-80. PMID:16434744
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