3HKI

Crystal structure of murine thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A.

Gandhi, P.S., Page, M.J., Chen, Z., Bush-Pelc, L., Di Cera, E.

(2009) J.Biol.Chem. 284: 24098-24105

  • DOI: 10.1074/jbc.M109.025403
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The thrombin mutant W215A/E217A (WE) is a potent anticoagulant both in vitro and in vivo. Previous x-ray structural studies have shown that WE assumes a partially collapsed conformation that is similar to the inactive E* form, which explains its dras ...

    The thrombin mutant W215A/E217A (WE) is a potent anticoagulant both in vitro and in vivo. Previous x-ray structural studies have shown that WE assumes a partially collapsed conformation that is similar to the inactive E* form, which explains its drastically reduced activity toward substrate. Whether this collapsed conformation is genuine, rather than the result of crystal packing or the mutation introduced in the critical 215-217 beta-strand, and whether binding of thrombomodulin to exosite I can allosterically shift the E* form to the active E form to restore activity toward protein C are issues of considerable mechanistic importance to improve the design of an anticoagulant thrombin mutant for therapeutic applications. Here we present four crystal structures of WE in the human and murine forms that confirm the collapsed conformation reported previously under different experimental conditions and crystal packing. We also present structures of human and murine WE bound to exosite I with a fragment of the platelet receptor PAR1, which is unable to shift WE to the E form. These structural findings, along with kinetic and calorimetry data, indicate that WE is strongly stabilized in the E* form and explain why binding of ligands to exosite I has only a modest effect on the E*-E equilibrium for this mutant. The E* --> E transition requires the combined binding of thrombomodulin and protein C and restores activity of the mutant WE in the anticoagulant pathway.

    Related Citations: 
    • The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket.
      Pineda, A.O.,Chen, Z.W.,Caccia, S.,Cantwell, A.M.,Savvides, S.N.,Waksman, G.,Mathews, F.S.,Di Cera, E.
      (2004) J.Biol.Chem. 279: 39824

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
A, D
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, E
258Mus musculusMutation(s): 2 
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 1
C, F
21Homo sapiensMutation(s): 0 
Gene Names: F2R (CF2R, PAR1, TR)
Find proteins for P25116 (Homo sapiens)
Go to Gene View: F2R
Go to UniProtKB:  P25116
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
B, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 231.419α = 90.00
b = 50.995β = 90.00
c = 80.540γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling
CNSrefinement
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance