Structure of a new alkaline serine protease (M-protease) from Bacillus sp. KSM-K16

An alkaline serine protease, M-protease, from Bacillus sp. KSM-K16 has been crystallized. Two morphologically different crystal forms were obtained. Crystal data of form 1: space group P2₁2₁2₁, a = 47.3, b = 62.5, c = 75.6 Å, V = 2.23 × 10⁵ ų, Z = 4 and V_m = 2.09 ų Da₋₁. Crystal data of form 2: space group P2₁2₁2₁, a = 75.82 (2), b = 57.79 (2), c = 54.19 (1) Å, V = 2.29 (2) × 10⁵ ų, Z = 4 and V_m = 2.15 ų Da₋₁. The crystal structure of M-protease in form 2 has been solved by molecular replacement using the atomic model of subtilisin Carlsberg (SBC) which is 60% homologous with M-protease, and refined to the crystallographic R-factor of 0.189 for 7004 reflections with F_o/σ(F) > 3 between 7 and 2.4 Å resolution. The final model of M-protease contains 1882 protein atoms, two calcium ions and 44 water molecules. The three-dimensional structure of M-protease is essentially similar to other subtilisins of known structure. The 269 C^α positions of M-protease have an r.m.s. difference of 1.06 Å with the corresponding positions of SBC. The crystal data of form 2 are close to those of SBC, though the structure determination of form 2 made it clear that it is not isomorphous to the crystal structure of SBC. The deletions of amino acids occur at the residues 36′ and 160′–163′ compared with SBC (numerals with primes show the numbering for SBC). The deletion of the four residues (160′–163′) may significantly affect the lack of isomorphism between M-protease and SBC.