Porphyromonas gingivalis has been associated with the development of adult periodontitis and cysteine proteinases with Arg- and Lys-specific activity have been implicated as major virulence factors. In a cell sonicate of P. gingivalis W50, a complex of non-covalently associated proteins has been previously characterized. This complex is composed of a 45 kDa Arg-specific, calcium-stabilized cysteine proteinase (PrtR45), a 48 kDa Lys-specific cysteine proteinase (PrtK48) and seven sequence-related adhesins designated PrtR44, PrtR15, PrtR17, PrtR27, PrtK39, PrtK15 and PrtK44, with all proteins being encoded by the two genes prtR and prtK. It has been proposed that these non-covalently associated complexes form extracellularly after autolytic processing of the PrtR and PrtK polyproteins, with the adhesins binding to the proteinases (PrtR45 and PrtK48) and autoaggregating. Another form of the cell-associated, Arg-specific, calcium-stabilized cysteine proteinase is described here. Designated PrtRII50, it is a discrete 50 kDa protein with no adhesin-association and has enzymic characteristics and an inhibitor/activator profile almost identical to PrtR45. The PrtRII50 proteinase is encoded as a preproprotein by a second gene, prtRII, with high sequence similarity to PrtR except that it lacks the C-terminal adhesin domains. A comparison of the deduced amino acid sequence of PrtRII50 with that of the adhesin-associated proteinases PrtR45 and PrtK48 revealed that PrtRII50 does not contain a C-terminal motif that is conserved in PrtR45 and PrtK48. Related motifs are also found in the adhesin domains of PrtR and PrtK. It is proposed that this conserved motif is an adhesin-binding motif (ABM) involved in association of the PrtR and PrtK proteinases and adhesins into large complexes, as the PrtR-PrtK proteinase-adhesin complex inactivated by N-alpha-p-tosyl-L-lysine chloromethyl ketone (TLCK) was shown to bind specifically to a synthetic peptide corresponding to the conserved motif in a competitive binding assay.