2PUX

Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4.

Bah, A.Chen, Z.Bush-Pelc, L.A.Mathews, F.S.Di Cera, E.

(2007) Proc.Natl.Acad.Sci.Usa 104: 11603-11608

  • DOI: 10.1073/pnas.0704409104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • It has been proposed that the cleaved form of protease-activated receptor 3 (PAR3) acts as a cofactor for thrombin cleavage and activation of PAR4 on murine platelets, but the molecular basis of this physiologically important effect remains elusive. ...

    It has been proposed that the cleaved form of protease-activated receptor 3 (PAR3) acts as a cofactor for thrombin cleavage and activation of PAR4 on murine platelets, but the molecular basis of this physiologically important effect remains elusive. X-ray crystal structures of murine thrombin bound to extracellular fragments of the murine receptors PAR3 ((38)SFNGGPQNTFEEFPLSDIE(56)) and PAR4 ((51)KSSDKPNPR downward arrow GYPGKFCANDSDTLELPASSQA(81), downward arrow = site of cleavage) have been solved at 2.0 and 3.5 A resolution, respectively. The cleaved form of PAR3, traced in the electron density maps from Gln-44 to Glu-56, makes extensive hydrophobic and electrostatic contacts with exosite I of thrombin through the fragment (47)FEEFPLSDIE(56). Occupancy of exosite I by PAR3 allosterically changes the conformation of the 60-loop and shifts the position of Trp-60d approximately 10 A with a resulting widening of the access to the active site. The PAR4 fragment, traced entirely in the electron density maps except for five C-terminal residues, clamps Trp-60d, Tyr-60a, and the aryl-binding site of thrombin with Pro-56 and Pro-58 at the P2 and P4 positions and engages the primary specificity pocket with Arg-59. The fragment then leaves the active site with Gly-60 and folds into a short helical turn that directs the backbone away from exosite I and over the autolysis loop. The structures demonstrate that thrombin activation of PAR4 may occur with exosite I available to bind cofactor molecules, like the cleaved form of PAR3, whose function is to promote substrate diffusion into the active site by allosterically changing the conformation of the 60-loop.


    Related Citations: 
    • Structural Basis of Na+ Activation mimicry in murine.
      Marino, F.,Chen, Z.,Ergenekan, C.E.,Bush, L.A.,Mathews, F.S.,Di Cera, E.
      (2007) J.Biol.Chem. --: --
    • Molecular Dissection of Na+ Binding to Thrombin.
      Pineda, A.O.,Carrell, C.J.,Bush, L.A.,Prasad, S.,Caccia, S.,Chen, Z.,Mathews, F.S.,Di Cera, E.
      (2004) J.Biol.Chem. 279: 31842


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
A
44Mus musculusMutation(s): 0 
Gene Names: F2 (Cf2)
EC: 3.4.21.5
Find proteins for P19221 (Mus musculus)
Go to Gene View: F2
Go to UniProtKB:  P19221
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
B
258Mus musculusMutation(s): 1 
Gene Names: F2 (Cf2)
EC: 3.4.21.5
Find proteins for P19221 (Mus musculus)
Go to Gene View: F2
Go to UniProtKB:  P19221
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteinase-activated receptor 3
C
13Mus musculusMutation(s): 0 
Gene Names: F2rl2 (Par3)
Find proteins for O08675 (Mus musculus)
Go to UniProtKB:  O08675
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.025α = 90.00
b = 48.188β = 106.23
c = 62.046γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance