1ZJD

Crystal Structure of the Catalytic Domain of Coagulation Factor XI in Complex with Kunitz Protease Inhibitor Domain of Protease Nexin II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Mutational Analyses of the Molecular Interactions between the Catalytic Domain of Factor XIa and the Kunitz Protease Inhibitor Domain of Protease Nexin 2

Navaneetham, D.Jin, L.Pandey, P.Strickler, J.E.Babine, R.E.Abdel-Meguid, S.S.Walsh, P.N.

(2005) J.Biol.Chem. 280: 36165-36175

  • DOI: 10.1074/jbc.M504990200

  • PubMed Abstract: 
  • Factor XIa (FXIa) is a serine protease important for initiating the intrinsic pathway of blood coagulation. Protease nexin 2 (PN2) is a Kunitz-type protease inhibitor secreted by activated platelets and a physiologically important inhibitor of FXIa. ...

    Factor XIa (FXIa) is a serine protease important for initiating the intrinsic pathway of blood coagulation. Protease nexin 2 (PN2) is a Kunitz-type protease inhibitor secreted by activated platelets and a physiologically important inhibitor of FXIa. Inhibition of FXIa by PN2 requires interactions between the two proteins that are confined to the catalytic domain of the enzyme and the Kunitz protease inhibitor (KPI) domain of PN2. Recombinant PN2KPI and a mutant form of the FXI catalytic domain (FXIac) were expressed in yeast, purified to homogeneity, co-crystallized, and the structure of the complex was solved at 2.6 angstroms (Protein Data Bank code 1ZJD). In this complex, PN2KPI has a characteristic, disulfide-stabilized double loop structure that fits into the FXIac active site. To determine the contributions of residues within PN2KPI to its inhibitory activity, selected point mutations in PN2KPI loop 1 11TGPCRAMISR20 and loop 2 34FYGGC38 were tested for their ability to inhibit FXIa. The P1 site mutation R15A completely abolished its ability to inhibit FXIa. IC50 values for the wild type protein and the remaining mutants were as follows: PN2KPI WT, 1.28 nM; P13A, 5.92 nM; M17A, 1.62 nM; S19A, 1.86 nM; R20A, 5.67 nM; F34A, 9.85 nM. The IC50 values for the M17A and S19A mutants were not significantly different from those obtained with wild type PN2KPI. These functional studies and activated partial thromboplastin time analysis validate predictions made from the PN2KPI-FXIac co-crystal structure and implicate PN2KPI residues, in descending order of importance, Arg15, Phe34, Pro13, and Arg20 in FXIa inhibition by PN2KPI.


    Related Citations: 
    • Molecular Interactions of Kunitz Protease Inhibitory Domain of Protease Nexin 2 and Catalytic Domain of Factor XIa
      Navaneetham, D.,Jin, L.,Babine, R.E.,Abdel-Meguid, S.S.,Walsh, P.N.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Sol Sherry Thrombosis Research Center, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catalytic Domain of Coagulation Factor XI
A
237Homo sapiensMutation(s): 3 
Gene Names: F11
EC: 3.4.21.27
Find proteins for P03951 (Homo sapiens)
Go to Gene View: F11
Go to UniProtKB:  P03951
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Kunitz Protease Inhibitory Domain of Protease Nexin II
B
57Homo sapiensMutation(s): 0 
Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens)
Go to Gene View: APP
Go to UniProtKB:  P05067
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.791α = 90.00
b = 92.791β = 90.00
c = 107.014γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
HKL-2000data collection
CNXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance