include a yeast protein. Another ancient family of cysteine proteases with relationship
to caspases are the insulinase-like enzymes.
Analysis of the domain architecture of the C.elegans caspase ced-3 provides another
interesting insight into the modularity of caspase evolution. The catalytic domain of
ced-3 resembles the catalytic domain of the mammalian executor caspases and reflects
the role of the ced-3 gene product as the major (if not sole) apoptotic caspase. By
contrast, the prodomain of the ced-3 protein does not resemble the executor caspases
at all, but is related to the caspase-9 CARD domain instead. Apparently, ced-3
combines the activation mode of mammalian initiator caspases with the cleavage
properties of caspase-3 and other downstream caspases.
4.2
The BIR domainThe BIR domain family, which plays an important role in the inhibition of caspases,
had first been identified as a repeat region in baculoviral apoptosis inhibitors, the IAP
proteins (Crook et al., 1993). While the viral IAP proteins carry a RING-finger at
the C-terminus, the N-terminal region contains two copies of a novel domain, which
is now known as BIR (for baculoviral IAP repeat). Soon, the first mammalian
homologs, XIAP, cIAP-1, and cIAP-2, were identified and found to have a role in
the regulation of apoptosis, too (Rothe et al., 1995; Duckett et al., 1996). The cellular
IAPs contain three copies of the BIR repeat, as well as a C-terminal RING-finger;
cIAP-1 and cIAP-2 additionally contain a copy of the CARD domain, for which no
binding partner has been identified yet. NAIP and ML-IAP are additional
mammalian IAPs, which have been identified more recently; ML-IAP contains only
a single BIR and a RING-finger, while NAIP is a much longer protein with three
BIRs and a NACHT-type ATPase domain (see Verhagen et al. [2001] for a survey).
By sequence analysis, the BIR family could be extended considerably, although
most of the newly identified proteins appear to have a role in the control of mitosis,
rather than in apoptosis. A well-known member of the latter class is survivin, a short,
single-BIR protein that was initially considered an apoptosis regulator. The average
BIR repeat spans approximately 70 residues and contains a conserved CxxCx15–
16Hx6–8C motif, which resembles a CCHC-type zinc finger. This idea was
confirmed by the three-dimensional structures of several BIRs from XIAP and cIAP-1
(Hinds et al., 1999; Sun et al., 1999), which show a coordinated Zn-ion embedded
in a typical Zn-finger fold. Of particular interest are the structures of caspase-3 and
caspase-7 in complex with the BIR domains of XIAP (Chai et al., 2001a; Riedl et al.,
2001b). Unexpectedly, the point of contact to the caspases does not lie within a
conserved BIR repeat but rather in the linker region upstream of BIR2. Another
interesting structure is that of XIAP’s BIR3 with the N-terminus of SMAC/DIABLO,
a negative regulator of the inhibitory activity of the IAP proteins (Liu et al., 2000;
Wu, G. et al., 2000). SMAC binds to a groove in the BIR3 domain and prevents
access of XIAP to the caspase. SMAC is liberated from the mitochondria, along with
cytochrome c, and has a proapoptotic effect by inhibiting the caspase inhibitors.
90 GENETICS OF APOPTOSIS