PDBsum entry 3b9f

Hydrolase/hydrolase inhibitor

PDB id: 3b9f

Contents

Protein chains

44 a.a. *

253 a.a. *

356 a.a. *

Ligands

NAG-FUC

SGN-IDS

SO4 ×3

GOL ×5

Waters ×523

* Residue conservation analysis

PDB id:

3b9f

Name:

Hydrolase/hydrolase inhibitor

Title:

1.6 a structure of the pci-thrombin-heparin complex

Structure:

Prothrombin. Chain: l. Fragment: thrombin light chain. Synonym: coagulation factor ii. Engineered: yes. Prothrombin. Chain: h. Fragment: thrombin heavy chain. Synonym: coagulation factor ii.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: f2. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: serpina5, pci, planh3, proci. Expression_system_taxid: 562

Resolution:

1.60Å R-factor: 0.208 R-free: 0.234

Authors:

W.Li,T.E.Adams,J.A.Huntington

Key ref:

W.Li et al. (2008). Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex. Proc Natl Acad Sci U S A, 105, 4661-4666. PubMed id: 18362344 DOI: 10.1073/pnas.0711055105

Date:

05-Nov-07 Release date: 22-Apr-08

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 44 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 253 a.a.*

Protein chain

Q9N2I2  (IPSP_BOVIN) -  Plasma serine protease inhibitor from Bos taurus

Seq: 404 a.a.

Struc: 356 a.a.*

* PDB and UniProt seqs differ at 86 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains L, H: E.C.3.4.21.5 - thrombin.
• Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

DOI no: 10.1073/pnas.0711055105

Proc Natl Acad Sci U S A 105:4661-4666 (2008)

PubMed id: 18362344

Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex.

W.Li, T.E.Adams, J.Nangalia, C.T.Esmon, J.A.Huntington.

ABSTRACT

Protein C inhibitor (PCI) is a serpin with many roles in biology, including a dual role as pro- and anticoagulant in blood. The protease specificity and local function of PCI depend on its interaction with cofactors such as heparin-like glycosaminoglycans (GAGs) and thrombomodulin (TM). Both cofactors significantly increase the rate of thrombin inhibition, but GAGs serve to promote the anticoagulant activity of PCI, and TM promotes its procoagulant function. To gain insight into how PCI recognition of thrombin is aided by these cofactors, we determined a crystallographic structure of the Michaelis complex of PCI, thrombin, and heparin to 1.6 A resolution. Thrombin interacts with PCI in an unusual fashion that depends on the length of PCI's reactive center loop (RCL) to align the heparin-binding sites of the two proteins. The principal exosite contact is engendered by movement of thrombin's 60-loop in response to the unique P2 Phe of PCI. This mechanism of communication between the active site of thrombin and its recognition exosite is previously uncharacterized and may relate to other thrombin substrate-cofactor interactions. The cofactor activity of heparin thus depends on the formation of a heparin-bridged Michaelis complex and substrate-induced exosite contacts. We also investigated the cofactor effect of TM, establishing that TM bridges PCI to thrombin through additional direct interactions. A model of the PCI-thrombin-TM complex was built and evaluated by mutagenesis and suggests distinct binding sites for heparin and TM on PCI. These data significantly improve our understanding of the cofactor-dependent roles of PCI in hemostasis.

Selected figure(s)

Figure 1.
Stereo ribbon diagrams of the PCI–thrombin–heparin Michaelis complex. (A) The complex is shown with PCI in the standard orientation with the yellow RCL on top and the red β-sheet A facing. The P1 Arg residue is shown as yellow rods, and the heparin binding helix H is at the back of the PCI in blue. Thrombin is on top, with its light chain colored magenta and the heavy chain colored cyan. The heparin disaccharide built into electron density is shown as green rods. (B) The same view as in A but colored according to temperature factor (B-factor from blue to red) to illustrate the mobile regions.

Figure 3.
Stereo representations of the PCI–thrombin complex bridged by a 14-mer heparin chain. (A) The ribbon diagram is rotated 150° relative to the view shown in Fig. 1A to illustrate the alignment of the heparin-binding regions. A 14-mer heparin chain (green rods) is placed onto the modeled disaccharide to yield a bridged complex with fully occupied heparin-binding sites. (B) The electrostatic surface of the complex in the same orientation as in A reveals the continuous basic (blue) heparin-binding sites of thrombin (Upper) and PCI (Lower).

Figures were selected by an automated process.