A serine protease was purified from suspension-cultured soybean cells, by a combination of anion exchange, hydrophobic interaction and affinity chromatography. A 90,000 M(r) subunit, which could be photoaffinity labelled with 3H-diisopropylfluorophosphate (DFP), was identified by SDS-polyacrylamide gel electrophoresis. The enzyme had a broad pH optimum from 5.5 to 8.5, and was strongly inhibited by antipain, leupeptin, aminoethylbenzenesulphonyl fluoride (AEBSF) and DFP, but not by soybean trypsin inhibitor. It cleaved several peptide 4-methylcoumaryl-7-amide derivatives after arginine or lysine residues. Mass spectroscopic analysis of oligopeptide digestion products indicated that the preferred cleavage positions were between paired arginine residues, or C-terminal to single arginine residues, depending on the oligopeptide substrate. Partial amino acid sequences from the purified protein showed sequence identity to bacterial protease II and prolyl peptidase, although the enzyme lacked prolyl endopeptidase activity. We discuss the possible involvement of the protease in plant defense responses.