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PDBsum entry 3b9f
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Hydrolase/hydrolase inhibitor
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PDB id
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3b9f
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Contents |
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44 a.a.
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253 a.a.
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356 a.a.
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References listed in PDB file
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Key reference
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Title
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Molecular basis of thrombin recognition by protein c inhibitor revealed by the 1.6-A structure of the heparin-Bridged complex.
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Authors
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W.Li,
T.E.Adams,
J.Nangalia,
C.T.Esmon,
J.A.Huntington.
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Ref.
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Proc Natl Acad Sci U S A, 2008,
105,
4661-4666.
[DOI no: ]
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PubMed id
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Abstract
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Protein C inhibitor (PCI) is a serpin with many roles in biology, including a
dual role as pro- and anticoagulant in blood. The protease specificity and local
function of PCI depend on its interaction with cofactors such as heparin-like
glycosaminoglycans (GAGs) and thrombomodulin (TM). Both cofactors significantly
increase the rate of thrombin inhibition, but GAGs serve to promote the
anticoagulant activity of PCI, and TM promotes its procoagulant function. To
gain insight into how PCI recognition of thrombin is aided by these cofactors,
we determined a crystallographic structure of the Michaelis complex of PCI,
thrombin, and heparin to 1.6 A resolution. Thrombin interacts with PCI in an
unusual fashion that depends on the length of PCI's reactive center loop (RCL)
to align the heparin-binding sites of the two proteins. The principal exosite
contact is engendered by movement of thrombin's 60-loop in response to the
unique P2 Phe of PCI. This mechanism of communication between the active site of
thrombin and its recognition exosite is previously uncharacterized and may
relate to other thrombin substrate-cofactor interactions. The cofactor activity
of heparin thus depends on the formation of a heparin-bridged Michaelis complex
and substrate-induced exosite contacts. We also investigated the cofactor effect
of TM, establishing that TM bridges PCI to thrombin through additional direct
interactions. A model of the PCI-thrombin-TM complex was built and evaluated by
mutagenesis and suggests distinct binding sites for heparin and TM on PCI. These
data significantly improve our understanding of the cofactor-dependent roles of
PCI in hemostasis.
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Figure 1.
Stereo ribbon diagrams of the PCI–thrombin–heparin
Michaelis complex. (A) The complex is shown with PCI in the
standard orientation with the yellow RCL on top and the red
β-sheet A facing. The P1 Arg residue is shown as yellow rods,
and the heparin binding helix H is at the back of the PCI in
blue. Thrombin is on top, with its light chain colored magenta
and the heavy chain colored cyan. The heparin disaccharide built
into electron density is shown as green rods. (B) The same view
as in A but colored according to temperature factor (B-factor
from blue to red) to illustrate the mobile regions.
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Figure 3.
Stereo representations of the PCI–thrombin complex bridged
by a 14-mer heparin chain. (A) The ribbon diagram is rotated
150° relative to the view shown in Fig. 1A to illustrate the
alignment of the heparin-binding regions. A 14-mer heparin chain
(green rods) is placed onto the modeled disaccharide to yield a
bridged complex with fully occupied heparin-binding sites. (B)
The electrostatic surface of the complex in the same orientation
as in A reveals the continuous basic (blue) heparin-binding
sites of thrombin (Upper) and PCI (Lower).
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