PDBsum entry 1fak

Blood clotting

PDB id: 1fak

Contents

Protein chains

108 a.a. *

251 a.a. *

183 a.a. *

55 a.a. *

Ligands

GLC

FUC

Metals

_CA ×2

Waters ×340

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of extracellular tissue factor complexed with factor viia inhibited with a bpti mutant.

Authors

E.Zhang, R.St charles, A.Tulinsky.

Ref.

J Mol Biol, 1999, 285, 2089-2104. [DOI no: 10.1006/jmbi.1998.2452]

PubMed id

9925787

Abstract

The event that initiates the extrinsic pathway of blood coagulation is the association of coagulation factor VIIa (VIIa) with its cell-bound receptor, tissue factor (TF), exposed to blood circulation following tissue injury and/or vascular damage. The natural inhibitor of the TF.VIIa complex is the first Kunitz domain of tissue factor pathway inhibitor (TFPI-K1). The structure of TF. VIIa reversibly inhibited with a potent (Ki=0.4 nM) bovine pancreatic trypsin inhibitor (BPTI) mutant (5L15), a homolog of TFPI-K1, has been determined at 2.1 A resolution. When bound to TF, the four domain VIIa molecule assumes an extended conformation with its light chain wrapping around the framework of the two domain TF cofactor. The 5L15 inhibitor associates with the active site of VIIa similar to trypsin-bound BPTI, but makes several unique interactions near the perimeter of the site that are not observed in the latter. Most of the interactions are polar and involve mutated positions of 5L15. Of the eight rationally engineered mutations distinguishing 5L15 from BPTI, seven are involved in productive interactions stabilizing the enzyme-inhibitor association with four contributing contacts unique to the VIIa.5L15 complex. Two additional unique interactions are due to distinguishing residues in the VIIa sequence: a salt bridge between Arg20 of 5L15 and Asp60 of an insertion loop of VIIa, and a hydrogen bond between Tyr34O of the inhibitor and Lys192NZ of the enzyme. These interactions were used further to model binding of TFPI-K1 to VIIa and TFPI-K2 to factor Xa, the principal activation product of TF.VIIa. The structure of the ternary protein complex identifies the determinants important for binding within and near the active site of VIIa, and provides cogent information for addressing the manner in which substrates of VIIa are bound and hydrolyzed in blood coagulation. It should also provide guidance in structure-aided drug design for the discovery of potent and selective small molecule VIIa inhibitors.

Figure 1.
Figure 1. Kunitz domain sequences. Only mutations of 5L15 with respect to BPTI are shown; the alanine mutation at the N-terminal is for expression purposes only. Black and shaded residues conserved and homologous, respect- ively, with respect to BPTI. The P5-P5 inhibitor binding sites are indicated.

Figure 4.
Figure 4. Stereoview of most of the polar interactions of 5L15 with VIIa. The 5L15 residues Asp11-Arg20 and Glu46 in atom colors, VIIa residues in blue; pertinent VIIa residues in chymotrypsinogen numbering. The hydrogen bonds are dual colored thin lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 2089-2104) copyright 1999.