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PDBsum entry 4hzh
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References listed in PDB file
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Key reference
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Title
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Crystal structure of prothrombin reveals conformational flexibility and mechanism of activation.
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Authors
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N.Pozzi,
Z.Chen,
D.W.Gohara,
W.Niu,
T.Heyduk,
E.Di cera.
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Ref.
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J Biol Chem, 2013,
288,
22734-22744.
[DOI no: ]
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PubMed id
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Abstract
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The zymogen prothrombin is composed of fragment 1 containing a Gla domain and
kringle-1, fragment 2 containing kringle-2, and a protease domain containing A
and B chains. The prothrombinase complex assembled on the surface of platelets
converts prothrombin to thrombin by cleaving at Arg-271 and Arg-320. The
three-dimensional architecture of prothrombin and the molecular basis of its
activation remain elusive. Here we report the first x-ray crystal structure of
prothrombin as a Gla-domainless construct carrying an Ala replacement of the
catalytic Ser-525. Prothrombin features a conformation 80 Å long, with
fragment 1 positioned at a 36° angle relative to the main axis of fragment 2
coaxial to the protease domain. High flexibility of the linker connecting the
two kringles suggests multiple arrangements for kringle-1 relative to the rest
of the prothrombin molecule. Luminescence resonance energy transfer measurements
detect two distinct conformations of prothrombin in solution, in a 3:2 ratio,
with the distance between the two kringles either fully extended (54 ± 2 Å)
or partially collapsed (≤34 Å) as seen in the crystal structure. A molecular
mechanism of prothrombin activation emerges from the structure. Of the two sites
of cleavage, Arg-271 is located in a disordered region connecting kringle-2 to
the A chain, but Arg-320 is well defined within the activation domain and is not
accessible to proteolysis in solution. Burial of Arg-320 prevents prothrombin
autoactivation and directs prothrombinase to cleave at Arg-271 first. Reversal
of the local electrostatic potential then redirects prothrombinase toward
Arg-320, leading to thrombin generation via the prethrombin-2 intermediate.
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Secondary reference #1
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Title
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Crystal structure of prethrombin-1.
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Authors
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Z.Chen,
L.A.Pelc,
E.Di cera.
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Ref.
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Proc Natl Acad Sci U S A, 2010,
107,
19278-19283.
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PubMed id
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