Figure 11. Details of caspase inhibition by XIAP.
(a) The catalytic cleft of caspase-3 in three different forms, i.e. inhibitor [CMK (chloromethyl ketone)]-bound (blue; PDB code 1CP3; [10]), active with free catalytic site (red; PDB 1QX3; [67]) or bound to BIR2 (grey; PDB 1I30; [255]), is highly conserved. There are no substantial alterations in main-chain or side-chain conformations with the docking of BIR2 to the cleft, and it is only when the tetrapeptide CMK inhibitor binds that Tyr-338 must rotate to accept the P2 side chain (green arrow). Consequently, the linker region of BIR2 appears perfectly adapted to the unliganded active form of caspase-7. (b) Superposition of the XIAP inhibitory region (pink sticks) and acetyl-DVAD-CMK (blue sticks) on the active-site cleft of caspase-3 from PDB file 1I30 [255]. The orientation is as for Figure 5 and shows the small 4 Å footprint made by acetyl-DVAD-CMK side-chains (cyan) compared with that made by XIAP side chains (magenta). Note the manifold interactions of the two residues in the BIR1–BIR2 linker that are critical for activity, i.e. Leu-141 and Asp-148 [256]. The former engages in van der Waals contacts with Tyr-338 and Phe-381h, while Asp-148 occupies the S4 pocket of the caspase, hydrogen-bonding in particular residues of the 341 substrate-binding loop (Arg-341, Ser-343 and Trp-348). In addition, the carboxylate of Asp-148 is clamped to the C-terminal residue of XIAP (BIR2), Arg-233 (not shown). (c) Crystal structure of BIR3 (green)-bound caspase-9 (blue) taken from PDB 1NW9 [122]. The BIR domain takes the position of the dimeric partner domain of caspase-9, essentially monomerizing the caspase, thus reversing the process of zymogen activation. The blow-up depicts a conformational relay upon BIR2 binding (green residues) that forces Phe-390 from the active conformation (red) to the inactive one (blue). A rotation of Phe-390 requires a compensatory rotation in Tyr-331 and a concomitant expulsion of the catalytic Cys-285 into a non-catalytic location. (d, e) The 4 Å footprint of caspase-9 residues (shaded magenta) in contact with either its dimeric partner caspase-9 (d) or BIR3 (e) at the dimer interface. Note that although the contacts are more extensive in the caspase-9 dimer, most of the crucial contacts are the same. An exception is the segment Ala-298–Phe-301, which forms the IBM interacting with the Smac pocket on BIR3. Rendered with PyMol.