Falcipain-2 (FP2) is a papain family cysteine protease and important hemoglobinase of erythrocytic Plasmodium falciparum parasites. Inhibitors of FP2 block hemoglobin hydrolysis and parasite development, suggesting that this enzyme is a promising target for antimalarial chemotherapy. FP2 and related plasmodial cysteine proteases have an unusual 14-aa motif near the C terminus of the catalytic domain. Recent solution of the structure of FP2 showed this motif to form a -hairpin that is distant from the enzyme active site and protrudes out from the protein. To evaluate the function of this motif, we compared the activity of the wild-type enzyme with that of a mutant lacking 10 aa of the motif ( ⌬10 FP2). ⌬10 FP2 had nearly identical activity to that of the wild-type enzyme against peptide substrates and the protein substrates casein and gelatin. However, ⌬10 FP2 demonstrated negligible activity against hemoglobin or globin. FP2 that was inhibited with trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane (FP2 E-64 ) formed a complex with hemoglobin, but ⌬10 FP2 E-64 did not, indicating that the motif mediates binding to hemoglobin independent of the active site. A peptide encoding the motif blocked hemoglobin hydrolysis, but not the hydrolysis of casein. Kinetics for the inhibition of ⌬10 FP2 were very similar to those for FP2 with peptidyl and protein inhibitors, but ⌬10 FP2 was poorly inhibited by the inhibitory prodomain of FP2. Our results indicate that FP2 utilizes an unusual motif for two specific functions, interaction with hemoglobin, its natural substrate, and interaction with the prodomain, its natural inhibitor.M alaria is one of the most important infectious diseases in the world. Plasmodium falciparum, the most virulent human malaria parasite, is believed to cause hundreds of millions of illnesses and over a million deaths each year (1). The control of malaria has been hindered by increasing resistance of malaria parasites to available drugs (2). New antimalarial drugs, ideally directed against new targets, are urgently needed (3). Among potential new targets for antimalarial therapy are proteases that hydrolyze hemoglobin. Intraerythrocytic malaria parasites break down hemoglobin in an acidic food vacuole to supply amino acids for parasite protein synthesis and to maintain osmotic stability (4, 5). Multiple proteases appear to participate in hemoglobin processing (6). Cysteine protease inhibitors block hemoglobin hydrolysis, indicating that cysteine proteases play a key role in this process (7). Falcipain-2 (FP2) and falcipain-3 (FP3) are papain-family cysteine proteases of erythrocytic stages of P. falciparum that localize to the food vacuole and readily hydrolyze hemoglobin (8, 9). Disruption of the FP2 gene led to the accumulation of undegraded hemoglobin in trophozoites, confirming a critical role for this enzyme in hemoglobin hydrolysis (10). Inhibition of FP2 and related proteases led to a block in parasite development (11, 12) and cured mice with murine malaria (13, 14), and efforts to develop...