IMP Research Report 2002

an extended conformation. Removal of higher order
structural elements would allow the substrate to
reinitiate folding after exit from DegP. Recruitment of
PDZ domains for the gating mechanism should permit
a direct coupling of substrate binding and translocation
within the DegP particle. Accordingly, the PDZ domains
may function as tentacular arms capturing substrates
and transferring them into the inner cavity. By binding
to the C-terminus or a -hairpin loop of a protein, the
PDZ domains could properly position the substrate for
threading it into the central cavity. After accessing this
Figure 1: Top and side views of the two hexamers observed in the
DegP crystals representing the open and closed form of the
molecule. The individual domains are colored differently with the
N-terminal domain in blue, the protease in green and the PDZ
domains in yellow and red, respectively. Both hexamers are
approximately equal in size having a height of 105 Å and a diameter
of 120 Å.
chamber, the fate of the unfolded protein depends on
the interplay of several active site loops (loops LA, L1,
L2, L3 using the protease nomenclature), which
regulate proteolytic activity.
The mobile sidewalls are constructed by twelve PDZ
domains, which mediate the opening and closing of
the particle and probably the initial interaction with
substrate. Further binding sites for misfolded proteins
are located within the inner cavity (Figure 2). Due to
the geometric constraints of this chamber, substrates
must be at least partially unfolded to enter. As in other
chaperones of known structure, the DegP cavity is lined
by hydrophobic residues. These residues form two
binding platforms, which have a pronounced structural
Figure 2: The internal cavity of DegP. For better illustration half cut
figures of the molecular surface were prepared from both top and
side views. The cutting area is shown in black. The chaperone-like
features of the inner cavity are the following: (Left) Plasticity.
Flexible portions are in red, whereas rigid areas are colored blue.
(Middle) Hydrophobicity. The inner cavity is mainly constructed by
hydrophobic residues, which are highlighted in cyan and green.
(Right) Size exclusion. To illustrate the geometric restriction of the
molecular compactor, a single -helix (yellow) was modeled into the
cavity.
flexibility as judged from their high thermal motion
factors. This plasticity should allow binding of diverse
polypeptides.
Future studies will concentrate on the characterization
of the protease form of DegP. We will aim to determine
high-resolution crystal structures with substrates and
Cage-forming proteases and chaperones can be
energy-dependent or energy-independent. In the former
group, ATPase activity is important for recognition of
target proteins, their dissociation and unfolding, their
translocation within the complex and various gating
mechanisms. The present crystal structure indicates
why these functions are not relevant for DegP. DegP
preferably degrades substrates, which are per se
inhibitors and extend the approach to the related DegQ
and DegS proteases. The search for additional
physiological substrates and for cellular effectors that
either inhibit or activate members of the DegP family
will contribute to our understanding of the fascinating
network controlling protein composition, which is
undoubtedly one of the key metabolic pathways of each
cell.
partially unfolded and which might accumulate under
extreme conditions. Alternatively, threading of substrate
through the inner chamber could promote unfolding into
Contact: clausen@imp.univie.ac.at
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