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Fig. 6.3 Exosite and ten residues on the periphery of MMP-12 active that tune specificity for and
interact with soluble elastin species and a collagen V-derived triple helical peptide. The sites of
interaction were mapped as burial within NMR-detected interfaces between the substrates and
inactivated MMP-12 and subsequently confirmed by mutagenesis to modulate specific activity for
these substrates (Bhaskaran et al.
2008
; Palmier et al.
2010
). Inactivated MMP-12(E219) is shown
as a surface plot with the active site running horizontally at left and the newly recognized exosite at
right. The backbone of the enzyme is faintly visible as a ribbon underneath the molecular surface.
Conservative mutations of red residues impair
K
m
for an elastin substrate and of
yellow residues
impair rate of catalytic turnover
k
cat
(Palmier et al.
2010
). Each lesion also impairs
k
cat
for the THP
substrate, and six of them impair
K
m
as well (Palmier et al.
2010
)
6.2.2 Exosites of Catalytic Domains
6.2.2.1 Exosites in a Catalytic Domain Exemplified by Thrombin
Complexes
The serine protease thrombin offers the perspective of a varied, rich, and thoroughly
characterized array of interactions with its positively charged, anion-binding exo-
sites I and II, also known as the “fibrinogen recognition exosite” and “heparin-
binding site”, respectively (Bode
2006
). Interactions at both of these exosites may
prove to be illustrative and conceptually relevant to matrix interactions with the
catalytic domain of MMPs. The binding of multiple partners makes complementary
contacts with exosite I. Complexes with thrombin inhibitors of hirudin, rhodniin,
and ornithodorin demonstrated each of the inhibitors to extend out of the active site
to wrap its acidic segments across basic exosite I, and make hydrophobic contacts
there too (Bode
2006
). Peptide epitopes from protease-activated receptors (PARs)
that are substrates similarly wrap from the active site around exosite I. Mutations of
