1znv | pdb_00001znv

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

spinqualitylabelsall models 1znv, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1znv is a 4 chain structure with sequence from Escherichia coli str. k-12 substr. w3110. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: NI, PO4 Related: 1mz8, 1pt3, 7cei, 1m08 Gene: cei7 (Escherichia coli str. K-12 substr. W3110) Resources: FirstGlance, OCA, RCSB, PDBsum Function [CEA7_ECOLI] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Colicin Colicin Immunity Protein

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