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J. Biol. Chem., Vol. 275, Issue 39, 30631-30637, September 29, 2000

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Imaging DNA Loops Induced by Restriction Endonuclease EcoRII
A SINGLE AMINO ACID SUBSTITUTION UNCOUPLES TARGET RECOGNITION FROM COOPERATIVE DNA INTERACTION AND CLEAVAGE^*

Merlind Mücke, Rudi Lurz^§, Petra Mackeldanz, Joachim Behlke^¶, Detlev H. Krüger, and Monika Reuter

From the  Institut für Virologie, Medizinische Fakultät der Humboldt-Universität (Charité), D-10098 Berlin, the ^§ Max-Planck-Institut für Molekulare Genetik, D-14159 Berlin, and the ^¶ Max-Delbrück-Centrum für Molekulare Medizin, D-13122 Berlin, Germany

EcoRII is a type IIE restriction endonuclease characterized by a highly cooperative reaction mechanism that depends on simultaneous binding of the dimeric enzyme molecule to two copies of its DNA recognition site. Transmission electron microscopy provided direct evidence that EcoRII mediates loop formation of linear DNA containing two EcoRII recognition sites. Specific DNA binding of EcoRII revealed a symmetrical DNase I footprint occupying 16-18 bases. Single amino acid replacement of Val²⁵⁸ by Asn yielded a mutant enzyme that was unaffected in substrate affinity and DNase I footprinting properties, but exhibited a profound decrease in cooperative DNA binding and cleavage activity. Because the electrophoretic mobility of the mutant enzyme-DNA complexes was significantly higher than that of the wild-type, we investigated if mutant V258N binds as a monomer to the substrate DNA. Analysis of the molecular mass of mutant V258N showed a high percentage of protein monomers in solution. The dissociation constant of mutant V258N confirmed a 350-fold decrease of the enzyme dimerization capability. We conclude that Val²⁵⁸ is located in a region of EcoRII involved in homodimerization. This is the first report of a specific amino acid replacement in a restriction endonuclease leading to the loss of dimerization and DNA cleavage while retaining specific DNA binding.

We dedicate this paper to Professor Walter Messer on the occasion of his 65th birthday.

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