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PDBsum entry 3g01
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References listed in PDB file
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Key reference
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Title
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Structure of granzyme c reveals an unusual mechanism of protease autoinhibition.
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Authors
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D.Kaiserman,
A.M.Buckle,
P.Van damme,
J.A.Irving,
R.H.Law,
A.Y.Matthews,
T.Bashtannyk-Puhalovich,
C.Langendorf,
P.Thompson,
J.Vandekerckhove,
K.Gevaert,
J.C.Whisstock,
P.I.Bird.
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Ref.
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Proc Natl Acad Sci U S A, 2009,
106,
5587-5592.
[DOI no: ]
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PubMed id
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Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above have
been manually determined.
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Abstract
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Proteases act in important homeostatic pathways and are tightly regulated. Here,
we report an unusual structural mechanism of regulation observed by the 2.5-A
X-ray crystal structure of the serine protease, granzyme C. Although the
active-site triad residues adopt canonical conformations, the oxyanion hole is
improperly formed, and access to the primary specificity (S1) pocket is blocked
through a reversible rearrangement involving Phe-191. Specifically, a register
shift in the 190-strand preceding the active-site serine leads to Phe-191
filling the S1 pocket. Mutation of a unique Glu-Glu motif at positions 192-193
unlocks the enzyme, which displays chymase activity, and proteomic analysis
confirms that activity of the wild-type protease can be released through
interactions with an appropriate substrate. The 2.5-A structure of the unlocked
enzyme reveals unprecedented flexibility in the 190-strand preceding the
active-site serine that results in Phe-191 vacating the S1 pocket. Overall,
these observations describe a broadly applicable mechanism of protease
regulation that cannot be predicted by template-based modeling or bioinformatic
approaches alone.
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Figure 2.
Granzyme C inactivation is caused by a register shift. (A)
Superposition of granzyme C (cyan) with human granzyme A
(yellow; PDB ID code 1ORF). The active-site triads are shown as
stick models: magenta, granzyme C; green, granzyme A. The blue
(granzyme C) and red (granzyme A) regions are enlarged in B. (B)
Stereoview of the register shift in granzyme C. The arrow
indicates the direction of register shift. (C) Stereoview of the
oxyanion hole. Trypsin in complex with BPTI (PDB ID code 2PTC)
was added to the superposition. BPTI residues 13–17 indicate
likely positioning of substrate P3–P2′. Dashed lines
indicate hydrogen bonds between granzyme C E193 carbonyl and
S195 amide and Oγ. The figures were rendered with PyMOL (32).
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Figure 4.
Stereochemistry of Glu-192. A stereo image of the F[o] −
F[c] omit map, contoured at 3.0 σ, generated after coordinate
refinement in the absence of residues Phe-191, Glu-192, and
Glu-193. These residues appear as stick models; the salt bridge
with Arg-99 is also shown for clarity.
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