4AFX

Crystal structure of the reactive loop cleaved ZPI in I2 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Basis for Catalytic Activation of Protein Z-Dependent Protease Inhibitor (Zpi) by Protein Z.

Huang, X.Yan, Y.TU, Y.Gatti, J.Broze, G.J.J.Zhou, A.Olson, S.T.

(2012) Blood 120: 1726

  • DOI: 10.1182/blood-2012-03-419598
  • Primary Citation of Related Structures:  4AJT, 4AJU

  • PubMed Abstract: 
  • The anticoagulant serpin, protein Z-dependent protease inhibitor (ZPI), is catalytically activated by its cofactor, protein Z (PZ), to regulate the function of blood coagulation factor Xa on membrane surfaces. The X-ray structure of the ZPI-PZ comple ...

    The anticoagulant serpin, protein Z-dependent protease inhibitor (ZPI), is catalytically activated by its cofactor, protein Z (PZ), to regulate the function of blood coagulation factor Xa on membrane surfaces. The X-ray structure of the ZPI-PZ complex has shown that PZ binds to a unique site on ZPI centered on helix G. In the present study, we show by Ala-scanning mutagenesis of the ZPI-binding interface, together with native PAGE and kinetic analyses of PZ binding to ZPI, that Tyr240 and Asp293 of ZPI are crucial hot spots for PZ binding. Complementary studies with protein Z-protein C chimeras show the importance of both pseudocatalytic and EGF2 domains of PZ for the critical ZPI interactions. To understand how PZ acts catalytically, we analyzed the interaction of reactive loop-cleaved ZPI (cZPI) with PZ and determined the cZPI X-ray structure. The cZPI structure revealed changes in helices A and G of the PZ-binding site relative to native ZPI that rationalized an observed 6-fold loss in PZ affinity and PZ catalytic action. These findings identify the key determinants of catalytic activation of ZPI by PZ and suggest novel strategies for ameliorating hemophilic states through drugs that disrupt the ZPI-PZ interaction.


    Organizational Affiliation

    Center for Molecular Biology of Oral Diseases, University of Illinois at Chicago, Chicago, IL 60612, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN Z DEPENDENT PROTEASE INHIBITOR
A
387Homo sapiensGene Names: SERPINA10 (ZPI)
Find proteins for Q9UK55 (Homo sapiens)
Go to Gene View: SERPINA10
Go to UniProtKB:  Q9UK55
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN Z DEPENDENT PROTEASE INHIBITOR
B
36Homo sapiensGene Names: SERPINA10 (ZPI)
Find proteins for Q9UK55 (Homo sapiens)
Go to Gene View: SERPINA10
Go to UniProtKB:  Q9UK55
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.850α = 90.00
b = 106.660β = 112.58
c = 81.163γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release