1ZNV

How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor

Summary for 1ZNV

• Entry DOI: 10.2210/pdb1znv/pdb
• Related: 1M08 1MZ8 1PT3 7CEI
• Descriptor: Colicin E7 immunity protein, Colicin E7, NICKEL (II) ION, ... (5 entities in total)
• Functional Keywords: h-n-h motif, ni-binding, protein-protein complex, endonuclease, hydrolase-protein binding complex, hydrolase/protein binding
• Biological source: Escherichia coli str. K12 substr.; More
• Total number of polymer chains: 4
• Total formula weight: 52579.93

Authors

Doudeva, L.G.,Huang, H.,Hsia, K.C.,Shi, Z.,Li, C.L.,Shen, Y.,Yuan, H.S. (deposition date: 2005-05-12, release date: 2006-03-14, Last modification date: 2023-10-25)

Primary citation

Doudeva, L.G.,Huang, H.,Hsia, K.C.,Shi, Z.,Li, C.L.,Shen, Y.,Cheng, Y.S.,Yuan, H.S.
Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+
Protein Sci., 15:269-280, 2006

PubMed Abstract: 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.

PubMed: 16434744
DOI: 10.1110/ps.051903406

Experimental method

X-RAY DIFFRACTION (2 Å)