3OSL

Structure of bovine thrombin-activatable fibrinolysis inhibitor in complex with tick carboxypeptidase inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.313 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Flexibility of the Thrombin-activatable Fibrinolysis Inhibitor Pro-domain Enables Productive Binding of Protein Substrates.

Valnickova, Z.Sanglas, L.Arolas, J.L.Petersen, S.V.Schar, C.Otzen, D.Aviles, F.X.Gomis-Ruth, F.X.Enghild, J.J.

(2010) J Biol Chem 285: 38243-38250

  • DOI: https://doi.org/10.1074/jbc.M110.150342
  • Primary Citation of Related Structures:  
    3OSL

  • PubMed Abstract: 

    We have previously reported that thrombin-activatable fibrinolysis inhibitor (TAFI) exhibits intrinsic proteolytic activity toward large peptides. The structural basis for this observation was clarified by the crystal structures of human and bovine TAFI. These structures evinced a significant rotation of the pro-domain away from the catalytic moiety when compared with other pro-carboxypeptidases, thus enabling access of large peptide substrates to the active site cleft. Here, we further investigated the flexible nature of the pro-domain and demonstrated that TAFI forms productive complexes with protein carboxypeptidase inhibitors from potato, leech, and tick (PCI, LCI, and TCI, respectively). We determined the crystal structure of the bovine TAFI-TCI complex, revealing that the pro-domain was completely displaced from the position observed in the TAFI structure. It protruded into the bulk solvent and was disordered, whereas TCI occupied the position previously held by the pro-domain. The authentic nature of the presently studied TAFI-inhibitor complexes was supported by the trimming of the C-terminal residues from the three inhibitors upon complex formation. This finding suggests that the inhibitors interact with the active site of TAFI in a substrate-like manner. Taken together, these data show for the first time that TAFI is able to form a bona fide complex with protein carboxypeptidase inhibitors. This underlines the unusually flexible nature of the pro-domain and implies a possible mechanism for regulation of TAFI intrinsic proteolytic activity in vivo.


  • Organizational Affiliation

    Center for Insoluble Protein Structure (inSPIN), Department of Molecular Biology, Science Park, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase B2
A, C
401Bos taurusMutation(s): 0 
EC: 3.4.17.20
UniProt
Find proteins for Q2KIG3 (Bos taurus)
Explore Q2KIG3 
Go to UniProtKB:  Q2KIG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2KIG3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase inhibitor
B, D
74Rhipicephalus bursaMutation(s): 0 
UniProt
Find proteins for Q5EPH2 (Rhipicephalus bursa)
Explore Q5EPH2 
Go to UniProtKB:  Q5EPH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EPH2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.313 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 279.1α = 90
b = 279.1β = 90
c = 279.1γ = 90
Software Package:
Software NamePurpose
ProDCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description