2ARQ

Human plasminogen activator inhibitor-2.[loop (66-98) deletion mutant] complexed with peptide n-acetyl-teaaagdggvmtgr-oh


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Plasminogen activator inhibitor-2 is highly tolerant to P8 residue substitution--implications for serpin mechanistic model and prediction of nsSNP activities

Di Giusto, D.A.Sutherland, A.P.Jankova, L.Harrop, S.J.Curmi, P.M.King, G.C.

(2005) J.Mol.Biol. 353: 1069-1080

  • DOI: 10.1016/j.jmb.2005.09.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The serine protease inhibitor (serpin) superfamily is involved in a wide range of cellular processes including fibrinolysis, angiogenesis, apoptosis, inflammation, metastasis and viral pathogenesis. Here, we investigate the unique mousetrap inhibitio ...

    The serine protease inhibitor (serpin) superfamily is involved in a wide range of cellular processes including fibrinolysis, angiogenesis, apoptosis, inflammation, metastasis and viral pathogenesis. Here, we investigate the unique mousetrap inhibition mechanism of serpins through saturation mutagenesis of the P8 residue for a typical family member, plasminogen activator inhibitor-2 (PAI-2). A number of studies have proposed an important role for the P8 residue in the efficient insertion and stabilisation of the cleaved reactive centre loop (RCL), which is a key event in the serpin inhibitory mechanism. The importance of this residue for inhibition of the PAI-2 protease target urinary plasminogen activator (urokinase, uPA) is confirmed, although a high degree of tolerance to P8 substitution is observed. Out of 19 possible PAI-2 P8 mutants, 16 display inhibitory activities within an order of magnitude of the wild-type P8 Thr species. Crystal structures of complexes between PAI-2 and RCL-mimicking peptides with P8 Met or Asp mutations are determined, and structural comparison with the wild-type complex substantiates the ability of the S8 pocket to accommodate disparate side-chains. These data indicate that the identity of the P8 residue is not a determinant of efficient RCL insertion, and provide further evidence for functional plasticity of key residues within enzyme structures. Poor correlation of observed PAI-2 P8 mutant activities with a range of physicochemical, evolutionary and thermodynamic predictive indices highlights the practical limitations of existing approaches to predicting the molecular phenotype of protein variants.


    Organizational Affiliation

    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasminogen activator inhibitor-2
A
382Homo sapiensMutation(s): 0 
Gene Names: SERPINB2 (PAI2, PLANH2)
Find proteins for P05120 (Homo sapiens)
Go to Gene View: SERPINB2
Go to UniProtKB:  P05120
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
14-mer from Plasminogen activator inhibitor-2
P
15Homo sapiensMutation(s): 1 
Gene Names: SERPINB2 (PAI2, PLANH2)
Find proteins for P05120 (Homo sapiens)
Go to Gene View: SERPINB2
Go to UniProtKB:  P05120
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
P
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.562α = 90.00
b = 104.126β = 90.00
c = 41.438γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
CCP4data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance