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Figure 3.
Figure 3. Structures
(A) Cartoon representation of the
OMP-peptide bound H198P/D320A DegS trimer (3GDV). The protease
domains of different subunits are colored green, cyan, and
magenta, except the L3 loop, which is colored black; the PDZ
domains are colored slate blue. The YQF OMP peptide and the
modified active-site serine (Mis^201) are shown in CPK
representation.
(B) Interactions near the active site of
the 3GDV structure. The O1P oxygen of Mis^201 (2F[o]-F[c]
electron density contoured at 1.6 σ) accepts hydrogen bonds
from the -NH groups of the oxyanion hole. Packing interactions
between the pyrrolidine ring of Pro^198 and the aromatic ring of
Tyr^162 help to stabilize the hydrogen bond between backbone
carbonyl oxygen and -NH groups of these amino acids and
therefore stabilize the functional active site.
(C) The
peptide-bound 1SOZ structure (Wilken et al., 2004) and our
peptide-bound 3GCO structure have very similar conformations
near the active site, except for the modification of Ser^201 in
3CGO and the His^198→Pro sequence change. In the 3GCO
structure, Leu^218 and Ser^219 in the S1-specificity pocket move
to some degree to accommodate the isopropyl moiety of Mis^201,
which mimics the P1 side chain of a substrate.
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