1VPI

PHOSPHOLIPASE A2 INHIBITOR FROM VIPOXIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-ray structure at 1.76 A resolution of a polypeptide phospholipase A2 inhibitor.

Devedjiev, Y.Popov, A.Atanasov, B.Bartunik, H.D.

(1997) J.Mol.Biol. 266: 160-172

  • DOI: 10.1006/jmbi.1996.0778

  • PubMed Abstract: 
  • The high resolution crystal structure of a natural PLA2 inhibitor has been determined by Patterson search methods. In the heterodimeric, neurotoxic complex, vipoxin, isolated from the venom of Bulgarian viper, PLA2 inhibitor represents the non-toxic ...

    The high resolution crystal structure of a natural PLA2 inhibitor has been determined by Patterson search methods. In the heterodimeric, neurotoxic complex, vipoxin, isolated from the venom of Bulgarian viper, PLA2 inhibitor represents the non-toxic subunit. The model was refined to a crystallographic R-factor of 15.5% for data between 6 and 1.76 A resolution. The packing of the inhibitor in the crystal reveals close contacts between the molecules, which are symmetry-related by the 2-fold axes of the lattice. These pairs associate as a crystallographic dimer, stabilized by a set of interactions, including van der Waals contacts between residues from symmetry-related pairs, denoted as the recognition site and the recognition surface. Residues Ph3, Trp31 and Tyr119 represent the recognition site of inhibitor which possibly fits to the hydrophobic wall of the target PLA2. The topology of the inhibitor represents the PLA2 type of folding: three long helices and a beta-hairpin. Superposition of the structure of the inhibitor shows an almost complete overlap with different mammalian and viper PLA2 in the backbone and in the position of the sidechains of the residues that belong to the active centre and the hydrophobic wall. A "lock and key" mechanism of recognition of its native PLA2 in gland cells and other toxic PLA2 in vitro has been suggested. The mechanism includes complementary "head to tail" interactions between the recognition site of the inhibitor and a recognition surface located on the hydrophobic wall of the target PLA2. Having a high spatial homology with the PLA2 family of enzymes but opposing their action, the inhibitor from vipoxin presents an example of a divergent evolution of an ancient PLA2. The presence of a space for binding calcium in the inhibitor is believed to be a rudiment and proof of a common origin with PLA2.


    Related Citations: 
    • Structure and Mechanism of Phospholipase A2
      Devedjiev, Y.,Popov, A.,Bartunik, H.-D.,Atanasov, B.
      (1994) Eur.Cryst.Meeting 15: 484
    • Crystals of Phospholipase A2 Inhibitor. The Non-Toxic Component of Vipoxin from the Venom of Bulgarian Viper (Vipera Ammodytes)
      Devedjiev, Y.,Atanasov, B.,Mancheva, I.,Aleksiev, B.
      (1993) J.Mol.Biol. 229: 1147
    • Solubility and Phase States of Vipoxin from the Venom of Bulgarian Viper (Vipera Ammodytes Ammodytes)
      Devedjiev, Y.D.,Mancheva, I.N.,Aleksiev, B.V.,Atanasov, B.P.
      (1989) Dokl.Bolg.Akad.Nauk 42: 91


    Organizational Affiliation

    Max-Planck Research Unit for Structural Molecular Biology, Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2 INHIBITOR
A
122Vipera ammodytes meridionalisMutation(s): 0 
Find proteins for P04084 (Vipera ammodytes meridionalis)
Go to UniProtKB:  P04084
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Work: 0.155 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.900α = 90.00
b = 68.900β = 90.00
c = 52.400γ = 90.00
Software Package:
Software NamePurpose
BLANCdata reduction
X-PLORphasing
BLANCdata scaling
X-PLORmodel building
IN-HOUSEdata reduction
LOCALdata collection
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other