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PDBsum entry 2afq
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Blood clotting,hydrolase
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PDB id
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2afq
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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 wild-Type human thrombin in the na+-Free state.
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Authors
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D.J.Johnson,
T.E.Adams,
W.Li,
J.A.Huntington.
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Ref.
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Biochem J, 2005,
392,
21-28.
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PubMed id
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Abstract
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Regulation of thrombin activity is critical for haemostasis and the prevention
of thrombosis. Thrombin has several procoagulant substrates, including
fibrinogen and platelet receptors, and essential cofactors for stimulating its
own formation. However, thrombin is also capable of serving an anticoagulant
function by activating protein C. The specificity of thrombin is primarily
regulated by binding to the cofactor TM (thrombomodulin), but co-ordination of
Na+ can also affect thrombin activity. The Na+-free form is often referred to as
'slow' because of reduced rates of cleavage of procoagulant substrates, but the
slow form is still capable of rapid activation of protein C in the presence of
TM. The molecular basis of the slow proteolytic activity of thrombin has
remained elusive, in spite of two decades of solution studies and many published
crystallographic structures. In the present paper, we report the first structure
of wild-type unliganded human thrombin grown in the absence of co-ordinating
Na+. The Na+-binding site is observed in a highly ordered position 6 A (1 A=0.1
nm) removed from that seen in the Na+-bound state. The movement of the Na+ loop
results in non-catalytic hydrogen-bonding in the active site and blocking of the
S1 and S2 substrate-binding pockets. Similar, if more dramatic, changes were
observed in a previous structure of the constitutively slow thrombin variant
E217K. The slow behaviour of thrombin in solutions devoid of Na+ can now be
understood in terms of an equilibrium between an inert species, represented by
the crystal structure described in the present paper, and an active form, where
the addition of Na+ populates the active state.
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