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PDBsum entry 1mh0
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Blood clotting
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PDB id
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1mh0
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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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Crystal structure of the anticoagulant slow form of thrombin.
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Authors
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A.O.Pineda,
S.N.Savvides,
G.Waksman,
E.Di cera.
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Ref.
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J Biol Chem, 2002,
277,
40177-40180.
[DOI no: ]
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PubMed id
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Abstract
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Using the thrombin mutant R77aA devoid of the site of autoproteolytic
degradation at exosite I, we have solved for the first time the structure of
thrombin free of any inhibitors and effector molecules and stabilized in the
Na(+)-free slow form. The slow form shows subtle differences compared with the
currently available structures of the Na(+)-bound fast form that carry
inhibitors at the active site or exosite I. The most notable differences are the
displacement of Asp-189 in the S1 specificity pocket, a downward shift of the
190-193 strand, a rearrangement of the side chain of Glu-192, and a significant
shift in the position of the catalytic Ser-195 that is no longer within
H-bonding distance from His-57. The structure of the slow form explains the
reduced specificity toward synthetic and natural substrates and suggests a
molecular basis for its anticoagulant properties.
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Figure 1.
Fig. 1. Backbone traces of thrombin in the slow (blue)
and fast (yellow) forms. The root mean square deviation between
the two structures is 0.5 Å. The structure of the slow
form refers to molecule A in the asymmetric unit. The structures
are portrayed in the "Bode orientation" (11) with the active
site at the center, the autolysis loop south, exosite I east,
and exosite II west. The slow form has residues 148-149e of the
autolysis loop not defined in the electron density map. The
remainder of the backbone trace is intact and documents no sites
of autoproteolytic cleavage, although the structure was solved
in the absence of inhibitors and crystal packing does not block
the active site. The fast form was derived from the coordinates
of the PPACK-inhibited thrombin (11), with the inhibitor removed
for clarity.
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Figure 3.
Fig. 3. A, environment of the catalytic triad in the slow
form, shown with the 2F[o]  F[c]
electron density maps contoured at 1.0  level. The
O-  atom
(B-factor = 27 Å2) of Ser-195 (B-factor = 27-33 Å2)
rotates 54° and moves 1.2 Å relative to the position
in the fast form inhibited with PPACK ( yellow). This change
pertains to the slow form because it is not seen in the
structure of the fast form inhibited with hirugen at exosite I
and with the active site free (12). The shift in the position of
Ser-195 breaks the H-bond with His-57. The interatomic distance
between the O- of Ser-195
and the N-  2
(B-factor = 36 Å2) of His-57 (B-factor = 30-37 Å2)
is 3.6 Å in the slow form, as opposed to 2.9 Å in
the fast form. B, comparison of the active site cleft in the
slow (colored by Corey-Pauling-Koltun) and fast form inhibited
with PPACK (yellow, from PDB entry 1PPB). Hydrogen bonds are
depicted as broken lines. Shown are the regions in contact with
substrate (orange, shown with the P1-P3 residues) that are
affected by the slow  fast
transition, i.e. the side chain of Asp-189 and Ser-195. Note how
the shift in the position of Ser-195 breaks the H-bond with
His-57, the imidazole group of which also rotates slightly
relative to the position in the fast form. The O- atom of
Ser-195 in the slow form moves too close to the C-  atom of the
P1 residue of substrate.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
40177-40180)
copyright 2002.
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