Cathepsin K is a lysosomal cysteine protease belonging
to the papain superfamily. It has been implicated as a
major mediator of osteoclastic bone resorption. Wild-type
human procathepsin K has been crystallized in a glycosylated
and a deglycosylated form. The latter crystals diffract
better, to 3.2 Å resolution, and contain four molecules
in the asymmetric unit. The structure was solved by molecular
replacement and refined to an R-factor of 0.194.
The N-terminal fragment of the proregion forms a globular
domain while the C-terminal segment is extended and shows
substantial flexibility. The proregion interacts with the
enzyme along the substrate binding groove and along the
proregion binding loop (residues Ser138–Asn156).
It binds to the active site in the opposite direction to
that of natural substrates. The overall binding mode of
the proregion to cathepsin K is similar to that observed
in cathepsin L, caricain, and cathepsin B, but there are
local differences that likely contribute to the specificity
of these proregions for their cognate enzymes. The main
observed difference is in the position of the short helix
α3p (67p–75p), which occupies the S′ subsites.
As in the other proenzymes, the proregion utilizes the
S2 subsite for anchoring by placing a leucine side chain
there, according to the specificity of cathepsin K toward
its substrate.