Structures of three polycystic kidney disease‐like domains from Clostridium histolyticum collagenases ColG and ColH

Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca 2+ ‐triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease‐like (PKD‐like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen‐binding domains (s3 in ColH and s3a and s3b in ColG). The X‐ray crystal structures of Ca 2+ ‐bound holo s2b (1.4 Å resolution, R = 15.0%, R free = 19.1%) and holo s2a (1.9 Å resolution, R = 16.3%, R free = 20.7%), as well as of Ca 2+ ‐free apo s2a (1.8 Å resolution, R = 20.7%, R free = 27.2%) and two new forms of N‐terminally truncated apo s2 (1.4 Å resolution, R = 16.9%, R free = 21.2%; 1.6 Å resolution, R = 16.2%, R free = 19.2%), are reported. The structurally similar PKD‐like domains resemble the V‐set Ig fold. In addition to a conserved β‐bulge, the PKD‐like domains feature a second bulge that also changes the allegiance of the subsequent β‐strand. This β‐bulge and the genesis of a Ca 2+ pocket in the archaeal PKD‐like domain suggest a close kinship between bacterial and archaeal PKD‐like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD‐like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a‐s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen‐binding mode previously found in s2b‐s3. B ‐factor analyses suggest that in the presence of Ca 2+ the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD‐like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD‐like domains in ColG and in ColH include Ca 2+ binding. Conserved residues not only interact with Ca 2+ , but also position the Ca 2+ ‐interacting water molecule. Ca 2+ aligns the N‐terminal linker approximately parallel to the major axis of the domain. Ca 2+ binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen‐targeting vehicles for various signal molecules.