Tannerella forsythia is a bacterial pathogen involved in periodontal disease. A cysteine protease PrtH has been characterized in this bacterium as a virulence factor. PrtH has the activity of detaching adherent cells from substratum, and the level of PrtH is associated with periodontal attachment loss. No reports exist on the structure, active site, and catalytic mechanism of PrtH. Using comparative sequence and structural analyses, we have identified homologs of PrtH in a number of bacterial and archaeal species. PrtH was found to be remotely related to caspases and other proteases with a caspase-like fold, such as gingipains from another periodontal pathogen Porphyromonas gingivalis. Our results offer structural and mechanistic insights into PrtH and its homologs, and help classification of this protease family.