Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 Å resolution

Abstract

X-ray diffraction data at atomic resolution to 0.98Å with 136380 observed unique reflections were collected using a high quality proteinase K crystals grown under microgravity conditions and cryocooled. The structure has been refined anisotropically with REFMAC and SHELX-97 with R-factors of 11.4 and 12.8%, and R_free-factors of 12.4 and 13.5%, respectively. The refined model coordinates have an overall rms shifts of 0.23 Å relative to the same structure determined at room temperature at 1.5 Åresolution. Several regions of the main chain and the side chains, which were not observed earlier have been seen more clearly. For example, amino acid 207, which was reported earlier as Ser has been clearly identified as Asp. Furthermore, side-chain disorders of 8 of 279 residues in the polypeptide have been identified. Hydrogen atoms appear as significant peaks in the F_o - F_c difference electron density map accounting for an estimated 46% of all hydrogen atoms at 2σ level. Furthermore, the carbon, nitrogen, and oxygen atoms can be differentiated clearly in the electron density maps. Hydrogen bonds are clearly identified in the serine protease catalytic triad (Ser-His-Asp). Furthermore, electron density is observed for an unusual, short hydrogen bond between aspartic acid and histidine in the catalytic triad. The short hydrogen bond, designated "catalytic hydrogen bond", occurs as part of an elaborate hydrogen bond network, involving Asp of the catalytic triad. Though unusual, these features seem to be conserved in other serine proteases. Finally there are clear electron density peaks for the hydrogen atoms associated with the Oγ of Ser 224 and Nδ1 of His 69.