M-protease is a subtilisin-family serine protease produced by an alkaliphilic Bacillus sp. strain. Optimal enzymatic activity of the protein occurs at pH 12.3. The crystal structure of M-protease (space group P2(1)2(1)2(1), a = 62.3, b = 75.5, c = 47.2 A) has been refined to a crystallographic R-factor of 17.2% at 1.5 A resolution. The alkaline adaptation mechanism of the enzyme was analyzed. Molecular phylogeny construction was used to determine the amino acid substitutions that occurred during the high-alkaline adaptation process. This analysis revealed a decrease in the number of negatively charged amino acids (aspartic acid and glutamic acid) and lysine residues and an increase in arginine and neutral hydrophilic amino acids (histidine, asparagine and glutamine) residues during the course of adaptation. These substitutions increased the isoelectric point of M-protease. Some of the acquired arginine residues form hydrogen bonds or ion pairs to combine both N- and C-terminal regions of M-protease. The substituted residues are localized to a hemisphere of the globular protein molecule where positional shifts of peptide segments, relative to those of the less alkaliphilic subtilisin Carlsberg, are observed. The biased distribution and interactions caused by the substituted residues seem to be responsible for stabilization of the conformation in a high-alkaline condition.