CD59 is a glycosylphosphatidylinositol-anchored protein that inhibits the assembly of the terminal complement membrane attack complex (MAC) pore, whereas Streptococcus intermedius intermedilysin (ILY), a pore forming cholesterol-dependent cytolysin (CDC), specifically binds to human CD59 (hCD59) to initiate the formation of its pore. The identification of the residues of ILY and hCD59 that form their binding interface revealed a remarkably deep correspondence between the hCD59 binding site for ILY and that for the MAC proteins C8␣ and C9. ILY disengages from hCD59 during the prepore to pore transition, suggesting that loss of this interaction is necessary to accommodate specific structural changes associated with this transition. Consistent with this scenario, mutants of hCD59 or ILY that increased the affinity of this interaction decreased the cytolytic activity by slowing the transition of the prepore to pore but not the assembly of the prepore oligomer. A signature motif was also identified in the hCD59 binding CDCs that revealed a new hCD59-binding member of the CDC family. Although the binding site on hCD59 for ILY, C8␣, and C9 exhibits significant homology, no similarity exists in their binding sites for hCD59. Hence, ILY and the MAC proteins interact with common amino acids of hCD59 but lack detectable conservation in their binding sites for hCD59.The cholesterol-dependent cytolysins (CDCs) 4 are a family of pore-forming toxins produced by a diverse group of Grampositive pathogens. Recently crystal structures of the membrane attack complex/perforin proteins complement C8␣, a C9-like protein from Photorhabdus luminescens, and mouse perforin (1-4) suggested that they are structurally and mechanistically related the CDCs (5-7) and may be ancient ancestors (8). Interestingly, this relationship between the CDCs and membrane attack complex/perforin proteins extends to other features of the complement system. Two members of the CDC family, intermedilysin (ILY) secreted by Streptococcus intermedius and vaginolysin (VLY) secreted by Gardnerella vaginalis, specifically bind to the human form of CD59 (hCD59), a glycosylphosphatidylinositol (GPI)-anchored terminal inhibitor of the mammalian complement membrane attack complex (MAC) (9), rather than cholesterol (10, 11). These CDCs bind to hCD59 to initiate the assembly of their oligomeric pore complex on the membrane of human cells (10), whereas the main function of CD59 is to block the assembly of the MAC pore on host cells, thereby protecting them from the lytic effects of activated complement MAC. Domain 4 of the CDCs mediates its interaction with cholesterol-rich membranes (12)(13)(14). Most CDCs use cholesterol as their receptor and specifically recognize its 3--hydroxy group. Recently Farrand et al. (15) defined the cholesterol recognition motif as a threonine/leucine pair located in loop 1 that is conserved in all members of the CDC family, including ILY and VLY. However, ILY initiates its interaction with the cell by binding to hCD59 (10) rather than chole...