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* Residue conservation analysis
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Enzyme class:
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Chains A, B, C, D:
E.C.3.4.21.5
- thrombin.
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Reaction:
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Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
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Biochem J
392:21-28
(2005)
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PubMed id:
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Crystal structure of wild-type human thrombin in the Na+-free state.
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D.J.Johnson,
T.E.Adams,
W.Li,
J.A.Huntington.
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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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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.D.Vogt,
A.Bah,
and
E.Di Cera
(2010).
Evidence of the E*-E equilibrium from rapid kinetics of Na+ binding to activated protein C and factor Xa.
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J Phys Chem B,
114,
16125-16130.
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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,
and
P.I.Bird
(2009).
Structure of granzyme C reveals an unusual mechanism of protease autoinhibition.
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Proc Natl Acad Sci U S A,
106,
5587-5592.
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PDB codes:
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J.A.Huntington
(2009).
Slow thrombin is zymogen-like.
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J Thromb Haemost,
7,
159-164.
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T.E.Adams,
W.Li,
and
J.A.Huntington
(2009).
Molecular basis of thrombomodulin activation of slow thrombin.
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J Thromb Haemost,
7,
1688-1695.
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PDB code:
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W.Niu,
Z.Chen,
L.A.Bush-Pelc,
A.Bah,
P.S.Gandhi,
and
E.Di Cera
(2009).
Mutant N143P reveals how Na+ activates thrombin.
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J Biol Chem,
284,
36175-36185.
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PDB codes:
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E.Di Cera
(2008).
Thrombin.
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Mol Aspects Med,
29,
203-254.
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J.A.Huntington
(2008).
How Na+ activates thrombin--a review of the functional and structural data.
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Biol Chem,
389,
1025-1035.
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K.W.Rickert,
P.Kelley,
N.J.Byrne,
R.E.Diehl,
D.L.Hall,
A.M.Montalvo,
J.C.Reid,
J.M.Shipman,
B.W.Thomas,
S.K.Munshi,
P.L.Darke,
and
H.P.Su
(2008).
Structure of human prostasin, a target for the regulation of hypertension.
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J Biol Chem,
283,
34864-34872.
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PDB codes:
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E.Di Cera,
M.J.Page,
A.Bah,
L.A.Bush-Pelc,
and
L.C.Garvey
(2007).
Thrombin allostery.
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Phys Chem Chem Phys,
9,
1291-1306.
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O.H.Olsen,
K.D.Rand,
H.Østergaard,
and
E.Persson
(2007).
A combined structural dynamics approach identifies a putative switch in factor VIIa employed by tissue factor to initiate blood coagulation.
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Protein Sci,
16,
671-682.
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P.E.Bock,
P.Panizzi,
and
I.M.Verhamme
(2007).
Exosites in the substrate specificity of blood coagulation reactions.
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J Thromb Haemost,
5,
81-94.
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A.Bah,
L.C.Garvey,
J.Ge,
and
E.Di Cera
(2006).
Rapid kinetics of Na+ binding to thrombin.
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J Biol Chem,
281,
40049-40056.
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A.O.Pineda,
Z.W.Chen,
A.Bah,
L.C.Garvey,
F.S.Mathews,
and
E.Di Cera
(2006).
Crystal structure of thrombin in a self-inhibited conformation.
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J Biol Chem,
281,
32922-32928.
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PDB code:
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J.R.Koeppe,
and
E.A.Komives
(2006).
Amide H/2H exchange reveals a mechanism of thrombin activation.
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Biochemistry,
45,
7724-7732.
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S.P.Bajaj,
A.E.Schmidt,
S.Agah,
M.S.Bajaj,
and
K.Padmanabhan
(2006).
High resolution structures of p-aminobenzamidine- and benzamidine-VIIa/soluble tissue factor: unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+, and Zn2+ sites in factor VIIa.
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J Biol Chem,
281,
24873-24888.
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PDB codes:
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V.De Filippis,
R.Frasson,
and
A.Fontana
(2006).
3-Nitrotyrosine as a spectroscopic probe for investigating protein protein interactions.
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Protein Sci,
15,
976-986.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
