Production of amyloid- protein (A) is initiated by a -secretase that cleaves the A precursor protein (APP) at the N terminus of A (the  site). A recently identified aspartyl protease, BACE, cleaves the  site and at residue 11 within the A region of APP. Here we show that BACE2, a BACE homolog, cleaves at the  site and more efficiently at a different site within A. The Flemish missense mutation of APP, implicated in a form of familial Alzheimer's disease, is adjacent to this latter site and markedly increases A production by BACE2 but not by BACE. BACE and BACE2 respond identically to conservative -site mutations, and alteration of a common active site Arg inhibits -site cleavage but not cleavage within A by both enzymes. These data suggest that BACE2 contributes to A production in individuals bearing the Flemish mutation, and that selective inhibition of these highly similar proteases may be feasible and therapeutically advantageous.T he amyloid- protein (A) is the principal component of the senile plaques characteristic of Alzheimer's disease (AD), and multiple lines of evidence have implicated cerebral accumulation of A in AD pathogenesis (1, 2). A is produced from the A precursor protein (APP) by two proteolytic events. A -secretase activity cleaves APP at the N terminus of A ( site) between amino acids Met-671 and Asp-672 (using the numbering of the 770-aa isoform of APP). Cleavage at the  site yields a membrane-associated APP fragment of 99 aa (C99). A second site within the transmembrane domain of C99 (␥ site) can then be cleaved by a ␥-secretase to release A, a peptide of 39-42 aa. APP can alternatively be cleaved within its A region, predominately at the ␣-secretase cleavage site of APP, to produce a C-terminal APP fragment of 83 aa (C83), which can also be further cleaved by ␥-secretase to produce a small secreted peptide, p3.A number of missense mutations in APP have been implicated in forms of early-onset familial AD. All of these are at or near one of the canonical cleavage sites of APP. Thus, the Swedish double mutation (K670N͞M671L) is immediately adjacent to the -cleavage site and increases the efficiency of -secretase activity, resulting in more total A (3). Any of three mutations at APP residue 717, near the ␥ site, increases the proportion of a more amyloidogenic 42-aa form of A [A(1-42)] relative to the more common 40-residue form [A(1-40)] (4-7).Two additional mutations of APP have been described which are close but not adjacent to the ␣ site. A mutation (A692G, A residue 21) in a Flemish family and a mutation (E693Q, A residue 22) in a Dutch family each have been implicated in distinct forms of familial AD (8-10). The Flemish mutation, in particular, presents as a syndrome of repetitive intracerebral hemorrhages or as an AD-type dementia. The neuropathological findings include senile plaques in the cortex and hippocampus, and usually multiple amyloid deposits in the walls of cerebral microvessels (8,11,12).Recently, a membrane-associated aspartyl protease, B...