gingivalis + -ain (cysteine protease suffix) = gingivain
Later, when researchers characterized the enzyme more thoroughly and found there were multiple distinct forms with different substrate specificities (arginine-specific and lysine-specific), the name was updated to "gingipain" to better reflect its role as a virulence factor of P. gingivalis, and the two subtypes (Rgp and Kgp) were defined.
The suffix "-pain" in gingipain also loosely follows the cysteine protease naming convention (like papain, calpain), while dropping the strict "-ain" form.