Figure 2.
FIGURE 2. Overlay of key residues in murine thrombin
(Corey-Pauling-Koltun, with carbon in yellow) and in the fast
form (Corey-Pauling-Koltun, with carbon in green) of human
thrombin (15). H-bonds (broken lines) refer to the murine
thrombin structure. The presence of Lys-222 in murine thrombin
stabilizes the conformation in a fast-like form. The O atom of
the catalytic Ser-195 is within H-bonding distance (3.05
Å) from His-57. This H-bond is present in the fast form of
the human enzyme (3.09 Å) but is broken (3.70 Å) in
the Na^+-free slow form (15). The side chain of Asp-189 in the
primary specificity pocket is oriented optimally for
coordination of Arg of substrate, as seen in the fast form. The
conformations of Asp-189 and Ser-195 are maintained by H-bonding
interactions mediated by water molecules, as in the fast form of
the human enzyme. However, only seven water molecules (red
balls) are present in this region of the murine thrombin
structure, as opposed to Na^+ (green ball) and 11 water
molecules (cyan balls) present in the fast form of the human
enzyme (15). The presence of Lys-222 in murine thrombin pushes
Arg-187 away and closer (2.55 Å) to Asp-221. The N atom of
Lys-222 and the O 1 atom of Asp-221
H-bond to water w153, which in turn stabilizes water w51 in a
position equivalent (<1 Å away) to the bound Na^+ in the
fast form (green ball) and in contact with the backbone oxygen
atoms of Arg-221a (2.77 Å) and Lys-224 (2.61 Å). The
H-bonding network around water w51 mimics that seen around the
bound Na^+ in the fast form of the human enzyme (15) and
establishes a connection to the O 2 atom of Asp-189 via
water w97. The O 1 atom of Asp-189 is
held in place by an H-bond with water w55 (2.74 Å).
Ser-195 is fixed in its orientation by a water-mediated contact
with the O 1 atom of Glu-192, with
water w63 positioned 3.19 Å away from the O atom of
Ser-195 and 2.82 Å away from the O 1 atom of Glu-192. The
only two water molecules, w141 and w142, between Asp-189 and
Ser-195 are too far away from either residue. Thus, murine
thrombin lacks the connectivity between the primary specificity
pocket and the catalytic triad seen in the fast form of the
human enzyme.
The above figure is reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
16355-16361)
copyright 2007.
atom of
the catalytic Ser-195 is within H-bonding distance (3.05
Å) from His-57. This H-bond is present in the fast form of
the human enzyme (3.09 Å) but is broken (3.70 Å) in
the Na^+-free slow form (15). The side chain of Asp-189 in the
primary specificity pocket is oriented optimally for
coordination of Arg of substrate, as seen in the fast form. The
conformations of Asp-189 and Ser-195 are maintained by H-bonding
interactions mediated by water molecules, as in the fast form of
the human enzyme. However, only seven water molecules (red
balls) are present in this region of the murine thrombin
structure, as opposed to Na^+ (green ball) and 11 water
molecules (cyan balls) present in the fast form of the human
enzyme (15). The presence of Lys-222 in murine thrombin pushes
Arg-187 away and closer (2.55 Å) to Asp-221. The N 
atom of
Lys-222 and the O 
1 atom of Asp-221
H-bond to water w153, which in turn stabilizes water w51 in a
position equivalent (<1 Å away) to the bound Na^+ in the
fast form (green ball) and in contact with the backbone oxygen
atoms of Arg-221a (2.77 Å) and Lys-224 (2.61 Å). The
H-bonding network around water w51 mimics that seen around the
bound Na^+ in the fast form of the human enzyme (15) and
establishes a connection to the O 
1 atom of Glu-192, with
water w63 positioned 3.19 Å away from the O