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Nucleic Acids Res. 2013 Nov;41(21):9812-24. doi: 10.1093/nar/gkt734. Epub 2013 Aug 19.

Increasing cleavage specificity and activity of restriction endonuclease KpnI.

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Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India, Department of Chemistry, New York University, NY, USA, Department of Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany, New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA and Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India.


Restriction enzyme KpnI is a HNH superfamily endonuclease requiring divalent metal ions for DNA cleavage but not for binding. The active site of KpnI can accommodate metal ions of different atomic radii for DNA cleavage. Although Mg(2+) ion higher than 500 μM mediates promiscuous activity, Ca(2+) suppresses the promiscuity and induces high cleavage fidelity. Here, we report that a conservative mutation of the metal-coordinating residue D148 to Glu results in the elimination of the Ca(2+)-mediated cleavage but imparting high cleavage fidelity with Mg(2+). High cleavage fidelity of the mutant D148E is achieved through better discrimination of the target site at the binding and cleavage steps. Biochemical experiments and molecular dynamics simulations suggest that the mutation inhibits Ca(2+)-mediated cleavage activity by altering the geometry of the Ca(2+)-bound HNH active site. Although the D148E mutant reduces the specific activity of the enzyme, we identified a suppressor mutation that increases the turnover rate to restore the specific activity of the high fidelity mutant to the wild-type level. Our results show that active site plasticity in coordinating different metal ions is related to KpnI promiscuous activity, and tinkering the metal ion coordination is a plausible way to reduce promiscuous activity of metalloenzymes.

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