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Figure 1
A ribbon model of the full-length collagenase structure (1fbl.pdb). The
prodomain would precede and include the portion labeled in the figure. The
catalytic domain is shown, with a highlighted region where the fibronectin-like
domain of the gelatinases is inserted.
II. 3-Dimensional Structure of MMPs
Page 173
Catalytic domain structures for fibroblast collagenase [22–25], neutrophil collagenase [26,27],
matrilysin [28], and stomelysin [29, 30] have all been determined and deposited in the Protein Data
Bank [31]. The catalytic domains of MMPs, as seen in the archetypal collagenase structure (shown as a
ribbon drawing [32] in Figure 1), consist of an upper 5-stranded β sheet flanked by two α helices on one
side of the active site cleft and a long loop that contains the Met-turn flanked by a single α helix on the
other side of the cleft.
The active-site groove as seen in the solvent-accessible surface [33] is an obvious structural feature
(Figure 2). The top wall of the cleft (as seen in Figure 2) is formed by the top strand of the β sheet and
the loop that contains the calcium binding site. The lower wall of the cleft is formed from the residues
on either side of the Met-turn. These residues can be considered as an interrupted strand which, together
with the substrate, complete the twisted β sheet of the catalytic domain. The bottom of the cleft is
formed by the second helix, which
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