Figure EV3. Graphic representation of C99 interactions with subsites in the γ‐secretase active site.

1. Comparison of the C99 interaction sites with the known interaction sites of transition state analog GSIs (Li et al, 2000b; Shelton et al, 2009) suggests that the binding site of these GSIs locates at the ε‐cleavage sites of C99. Using differently placed photoreactive benzophenone moieties in the FFLF peptide‐based L‐685,458 GSI derivatives L‐852,646 (646), GY4, JC8, and L‐852,505 (505), the S2‐S1′ pockets were previously located to the PS1 NTF (Li et al, 2000b; Shelton et al, 2009). In addition, the S3′ pocket could almost exclusively be located to the PS1 CTF by GSI 505 (Li et al, 2000b; Shelton et al, 2009). Preferential location of the S3′ pocket to the PS1 CTF was also observed for the related GSI III‐63 (Kornilova et al, 2005). As determined here, the only sites of C99 that crosslinked to the PS1 CTF were residues M51, L52, and K54.
2. Combining the information given in (A), we fitted the S3′ pocket in the PS1 CTF determined by GSI 505 with each of these residues (fit 1, 2, and 3). By this analysis, the hydroxyl group of GSI 505 and thus the γ‐secretase active site were found to locate at the ε48, the major ε49, and the very minor ε51 site, respectively.

Data information: Subsite pockets in the PS1 CTF are highlighted in light blue according to the subunit color code used. Red arrow indicates the location of the γ‐secretase active site.