PDBsum entry 1zr0

Hydrolase/blood clotting

PDB id: 1zr0

Contents

Protein chains

223 a.a. *

63 a.a. *

Metals

_CA ×2

Waters ×519

* Residue conservation analysis

PDB id:

1zr0

Name:

Hydrolase/blood clotting

Title:

Crystal structure of kunitz domain 1 of tissue factor pathway inhibitor-2 with bovine trypsin

Structure:

Cationic trypsin. Chain: a, c. Synonym: beta-trypsin. Tissue factor pathway inhibitor 2. Chain: b, d. Fragment: kunitz domain 1 (kd1). Synonym: tfpi-2. Placental protein 5. Pp5. Engineered: yes. Other_details: numbered according to the bpti numbering system

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Homo sapiens. Human. Organism_taxid: 9606. Gene: tfpi2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.231 R-free: 0.296

Authors:

A.E.Schmidt,H.S.Chand,D.Cascio,W.Kisiel,S.P.Bajaj

Key ref:

A.E.Schmidt et al. (2005). Crystal structure of Kunitz domain 1 (KD1) of tissue factor pathway inhibitor-2 in complex with trypsin. Implications for KD1 specificity of inhibition. J Biol Chem, 280, 27832-27838. PubMed id: 15932872 DOI: 10.1074/jbc.M504105200

Date:

18-May-05 Release date: 07-Jun-05

Protein chains

P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus

Seq: 246 a.a.

Struc: 223 a.a.*

Protein chains

P48307  (TFPI2_HUMAN) -  Tissue factor pathway inhibitor 2 from Homo sapiens

Seq: 235 a.a.

Struc: 63 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1074/jbc.M504105200

J Biol Chem 280:27832-27838 (2005)

PubMed id: 15932872

Crystal structure of Kunitz domain 1 (KD1) of tissue factor pathway inhibitor-2 in complex with trypsin. Implications for KD1 specificity of inhibition.

A.E.Schmidt, H.S.Chand, D.Cascio, W.Kisiel, S.P.Bajaj.

ABSTRACT

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.

Selected figure(s)

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 .

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.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 27832-27838) copyright 2005.

Figures were selected by an automated process.