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PDBsum entry 1zr0
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Hydrolase/blood clotting
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PDB id
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1zr0
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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 kunitz domain 1 (kd1) of tissue factor pathway inhibitor-2 in complex with trypsin. Implications for kd1 specificity of inhibition.
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Authors
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A.E.Schmidt,
H.S.Chand,
D.Cascio,
W.Kisiel,
S.P.Bajaj.
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Ref.
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J Biol Chem, 2005,
280,
27832-27838.
[DOI no: ]
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PubMed id
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Abstract
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Kunitz domain 1 (KD1) of tissue factor pathway inhibitor-2 inhibits trypsin,
plasmin, and factor VIIa (FVIIa)/tissue factor with Ki values of 13, 3, and 1640
nM, respectively. To investigate the molecular specificity of KD1, crystals of
the complex of KD1 with bovine beta-trypsin were obtained that diffracted to 1.8
A. The P1 residue Arg-15 (bovine pancreatic trypsin inhibitor numbering) in KD1
interacts with Asp-189 (chymotrypsin numbering) and with the carbonyl oxygens of
Gly-219 and Ogamma of Ser-190. Leu-17, Leu-18, Leu-19, and Leu-34 in KD1 make
van der Waals contacts with Tyr-39, Phe-41, and Tyr-151 in trypsin, forming a
hydrophobic interface. Molecular modeling indicates that this complementary
hydrophobic patch is composed of Phe-37, Met-39, and Phe-41 in plasmin, whereas
in FVIIa/tissue factor, it is essentially absent. Arg-20, Tyr-46, and Glu-39 in
KD1 interact with trypsin through ordered water molecules. In contrast,
insertions in the 60-loop in plasmin and FVIIa allow Arg-20 of KD1 to directly
interact with Glu-60 in plasmin and Asp-60 in FVIIa. Moreover, Tyr-46 in KD1
electrostatically interacts with Lys-60A and Arg-60D in plasmin and Lys-60A in
FVIIa. Glu-39 in KD1 interacts directly with Arg-175 of the basic patch in
plasmin, whereas in FVIIa, such interactions are not possible. Thus, the
specificity of KD1 for plasmin is attributable to hydrophobic and direct
electrostatic interactions. For trypsin, hydrophobic interactions are intact,
and electrostatic interactions are weak, whereas for FVIIa, hydrophobic
interactions are missing, and electrostatic interactions are partially intact.
These findings provide insight into the protease selectivity of KD1.
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Figure 2.
FIG. 2. Hydrophobic core in KD1. A, residues comprising the
hydrophobic core in KD1. KD1 is shown as a ribbon with  -strands
in yellow. Carbons are green, oxygens are red, and nitrogens are
blue. The internal hydrophobic core of KD1 is composed of Leu-9,
Tyr-11, Tyr-21, Tyr-22, Phe-33, and Tyr-35. B, electron density
surrounding some of the hydrophobic core residues in KD1. The
hydrophobic core residues that are depicted are Leu-9, Tyr-11,
Tyr-22, and Phe-33, and water molecules in the vicinity are
shown as red spheres. The electron density is a 2F[o] - F[c] map
contoured at 1.2  .
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Figure 5.
FIG. 5. Model of KD1 with plasmin. Plasmin is shown with
cyan ribbons, and KD1 is shown with yellow ribbons. A,
KD1·plasmin hydrophobic interface. The hydrophobic patch
in KD1 composed of Leu-17, Leu-18, Leu-19, and Leu-34 is shown
interacting with a hydrophobic patch in plasmin consisting of
Phe-37 {583}, Met-39 {585}, and Phe-41 {587}. B, Arg-20 and
Tyr-46 of KD1 interactions with plasmin. As compared with
interactions in the KD1·trypsin complex, Arg-20 of KD1
directly interacts with Glu-60 {606} of plasmin, and Tyr-46 of
KD1 interacts with Lys-60A {607} and Arg-60D {610} in plasmin.
C, Glu-39 of KD1 interactions with plasmin. Glu-39 of the acidic
patch in KD1 interacts directly with Arg-175 {719} and possibly
through water molecules to Arg-100 {644} and Arg-221 {767} of
the basic patch in plasmin.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
27832-27838)
copyright 2005.
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