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PDBsum entry 1a0h
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Hydrolase/hydrolase inhibitor
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PDB id
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1a0h
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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New insights into the regulation of the blood clotting cascade derived from the X-Ray crystal structure of bovine meizothrombin des f1 in complex with ppack.
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Authors
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P.D.Martin,
M.G.Malkowski,
J.Box,
C.T.Esmon,
B.F.Edwards.
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Ref.
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Structure, 1997,
5,
1681-1693.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: The conversion of prothrombin to thrombin by factor Xa is the
penultimate step in the blood clotting cascade. In vivo, where the conversion
occurs primarily on activated platelets in association with factor Va and Ca2+
ions, meizothrombin is the major intermediate of the two step reaction.
Meizothrombin rapidly loses the fragment 1 domain (F1) by autolysis to become
meizothrombin des F1 (mzTBN-F1). The physiological properties of mzTBN-F1 differ
dramatically from those of thrombin due to the presence of prothrombin fragment
2 (F2), which remains covalently attached to the activated thrombin domain in
mzTBN-F1. RESULTS: The crystal structure of mzTBN-F1 has been determined at 3.1
A resolution by molecular replacement, using only the thrombin domain, and
refined to R and Rfree values of 0.205 and 0.242, respectively. The protease
active site was inhibited with D-Phe-Pro-Arg-chloromethylketone (PPACK) to
reduce autolysis. The mobile linker chain connecting the so-called kringle and
thrombin domains and the first two N-acetylglucosamine residues attached to the
latter were seen in electron-density maps improved with the program SQUASH.
Previously these regions had only been modeled. CONCLUSIONS: The F2 kringle
domain in mzTBN-F1 is bound to the electropositive heparin-binding site on
thrombin in an orientation that is systematically shifted and has significantly
more interdomain contacts compared to a noncovalent complex of free F2 and free
thrombin. F2 in mzTBN-F1 forms novel hydrogen bonds to the carbohydrate chain of
thrombin and perhaps stabilizes a unique, rigid conformation of the
gamma-autolysis loop through non-local effects. The F2 linker chain, which does
not interfere with the active site or fibrinogen-recognition site, is arranged
so that the two sites cleaved by factor Xa are separated by 36 A. The two
mzTBN-F1 molecules in the asymmetric unit share a tight 'dimer' contact in which
the active site of one molecule is partially blocked by the F2 kringle domain of
its partner. This interaction suggests a new model for prothrombin organization.
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Figure 2.
Figure 2. The interface between the F2 kringle domain and
thrombin. Residues between the thrombin (red) and F2 kringle
(blue) domains that are within 5 Å of one another are shown in
stereo. Hydrogen bonds are shown as dashed lines (green). For
clarity, residues are identified only by their prothrombin
sequence position.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
1681-1693)
copyright 1997.
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