Genetics of Apoptosis

contain a pair of death effector domains (DEDs) in their prodomain regions (reviewed
in Kumar, 1999; Kumar and Colussi, 1999; Shi, 2002) (Figure 1). A number of other
caspases, including C. elegans CSP-1 and CSP-2, and Drosophila STRICA, have long
prodomains, lacking any CARD or DED (Shaham, 1998; Doumanis et al., 2001).
While the CARDs and DEDs in some caspases clearly play a role in caspase activation,
the function of long prodomains in CSP-1, CSP-2, and STRICA is currently unclear.

3.

Caspase structure

Structures of several active caspases, including caspases-1, -3, -8, and -9, and caspase-7
zymogen, have been determined (Walker et al., 1994; Wilson et al., 1994; Mittl et
al., 1997; Rotonda et al., 1996; Blanchard et al., 1999; Watt et al., 1999; Renatus et
al., 2001; Chai et al., 2001b; Riedl et al., 2001b; reviewed in Shi, 2001). The
functional caspase unit is a homodimer, with each monomer consisting of a large and
a small subunit. The active site Cys is located within the large subunit, whereas the
residues that form the S1 subsite are derived from both large and small subunits.
Homodimerization between the two caspase molecules is mediated by hydrophobic
interactions with six antiparallel β strands from each catalytic subunit, forming a
contiguous 12-stranded β sheet. The recently determined procaspase-7 structure
shows that the overall fold of the homodimeric procaspase-7 is similar to the active
tetrameric caspase-7 in that each monomer is organized in two structured subdomains
connected by partially flexible linkers (Chai et al., 2001b; Riedl et al., 200 la).
However, in the procaspase, the linker asymmetrically occupies and blocks the central
cavity that is normally present in the active caspases. This leads to the inability of the
procaspase molecule to interact with the substrate or inhibitor. Following the
processing of the zymogen, the cleavage within the linkers results in conformational
changes that govern the formation of an active site (Chai et al., 2001b; Riedl et al.,
2001b). Thus, in the case of effector caspases, such as caspase-7 (and perhaps also
caspase-3), the cleavage of the zymogen into two subunits is necessary for the
activation of the enzyme. The zymogen structure of any of the initiator caspases has
not been solved.

4.

Substrate specificity of caspases

The substrate binding site of active caspases is formed by four loops L1-L4, which
determine the substrate sequence specificity of various caspases (Figure 1). Of these
loops, L2 and L4 are highly variable among different caspases, whereas L1 and L3
are of relatively similar length. The binding pockets for the P4-P1 residues in the
substrates (termed S4-S1 subsites) are mostly located between L1, L3, and L4
(reviewed in Shi, 2001). The minimum substrate requirement for caspase-mediated
cleavage is a tetrapeptide with an Asp residue in P1 position, with the P4-P2 residues
detemining caspase target specificities. However, there are exceptions to this case. For

THE ROLE OF CASPASES IN APOPTOSIS 35