A gene encoding a Ca(2+)-dependent nuclease (AtCaN2) consisting of 226 amino acids from Arabidopsis thaliana was isolated. The AtCaN2 gene was expressed in Escherichia coli as a His fusion protein. The His-AtCaN2 fusion protein was purified by affinity chromatography using a Ni-NTA column. Western blot analysis using an anti-His antibody showed that the His-AtCaN2 fusion protein was not degraded. The nuclease activity of the His-AtCaN2 fusion protein was highest at 37°C, required a neutral or weakly-alkaline environment, and was stimulated by Ca(2+) and Mg(2+), but inhibited by Zn(2+) and high concentration of Mn(2+).