Ca(2+)-, Mg(2+)-dependent wheat endonuclease WEN1 with molecular mass of about 27 kDa was isolated from coleoptyles. Methylated DNA of lambda phage grown on E. coli dam(+), dcm(+) cells was hydrolyzed by WEN1 more effectively than DNA of phage grown on dam(-), dcm(-) cells. Two pH activity maxima (pH 6.5-7.5 and 9.0-10.5) were observed when double-stranded DNA was hydrolyzed. WEN1 is stable at elevated temperatures (65 degrees C ) and in wide range of pH values. WEN1 is activated by S-adenosyl-L-methionine, S-adenosyl-L-homocysteine and S-isobutyladenosine. It is a first case to show that higher eukaryote endonuclease discriminates between DNA of various methylation status and is modulated by S-AdoMet and its analogs.