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PDBsum entry 3gds
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Hydrolase/hydrolase activator
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PDB id
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3gds
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References listed in PDB file
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Key reference
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Title
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Omp peptides activate the degs stress-Sensor protease by a relief of inhibition mechanism.
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Authors
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J.Sohn,
R.A.Grant,
R.T.Sauer.
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Ref.
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Structure, 2009,
17,
1411-1421.
[DOI no: ]
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PubMed id
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Abstract
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In the E. coli periplasm, C-terminal peptides of misfolded outer-membrane porins
(OMPs) bind to the PDZ domains of the trimeric DegS protease, triggering
cleavage of a transmembrane regulator and transcriptional activation of stress
genes. We show that an active-site DegS mutation partially bypasses the
requirement for peptide activation and acts synergistically with mutations that
disrupt contacts between the protease and PDZ domains. Biochemical results
support an allosteric model, in which these mutations, active-site modification,
and peptide/substrate binding act in concert to stabilize proteolytically active
DegS. Cocrystal structures of DegS in complex with different OMP peptides reveal
activation of the protease domain with varied conformations of the PDZ domain
and without specific contacts from the bound OMP peptide. Taken together, these
results indicate that the binding of OMP peptides activates proteolysis
principally by relieving inhibitory contacts between the PDZ domain and the
protease domain of DegS.
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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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Figure 5.
Figure 5. Models for DegS Activation
(A) The
inhibition-relief model posits an equilibrium between free
inactive trimers (open squares) and free active trimers (open
circles). OMP peptides bind to both states (shaded circles or
squares) and shift the equilibrium toward the active form
because they bind more tightly to this conformation than the
inactive conformation.
(B) The peptide-activation model
posits that different OMP peptides stabilize slightly different
DegS conformations, in which the precise activity depends on the
identity of the penultimate side-chain of the bound peptide.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2009,
17,
1411-1421)
copyright 2009.
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