1PC9

Crystal Structure of BnSP-6, a Lys49-Phospholipase A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of BnSP-7 and BnSP-6, two Lys49-phospholipases A(2): quaternary structure and inhibition mechanism insights.

Magro, A.J.Soares, A.M.Giglio, J.R.Fontes, M.R.M.

(2003) Biochem.Biophys.Res.Commun. 311: 713-720

  • Primary Citation of Related Structures:  1PA0

  • PubMed Abstract: 
  • Phospholipases A(2) are components of Bothrops venoms responsible for disruption of cell membrane integrity via hydrolysis of its phospholipids. A class of PLA(2)-like proteins has been described which despite PLA(2) activity on artificial substrate, ...

    Phospholipases A(2) are components of Bothrops venoms responsible for disruption of cell membrane integrity via hydrolysis of its phospholipids. A class of PLA(2)-like proteins has been described which despite PLA(2) activity on artificial substrate, due to a D49K mutation, is still highly myonecrotic. This work reports the X-ray structure determination of two Lys49-PLA(2)s from Bothrops neuwiedi pauloensis (BnSP-7 and BnSP-6) and, for the first time, the comparison of eight dimeric Lys49-PLA(2)s. This comparison reveals that there are not just two ("open" and "closed") but at least six different conformations. The binding of fatty acid observed in three recent Lys49-PLA(2) structures seems to be independent of their quaternary conformation. Cys29 polarization by Lys122 is not significant for BnSP-7 and BnSP-6 or other structures not bound by fatty acids. These structures may be in an "active" state when nothing is bound to them and the Lys122/Cys29 interactions are weak or absent.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of BnSP-6, a Myotoxic Phospholipase A2 from Bothrops neuwiedi Venom
      Fontes, M.R.M.,Monteiro, L.E.,Soares, A.M.,Rodrigues, V.M.,da Silva, R.J.,Giglio, J.R.
      (2000) Protein Pept.Lett. 7: 421


    Organizational Affiliation

    Departamento de Física e Biofísica, IB, UNESP, Botucatu-SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BnSP-6
A, B
121Bothrops pauloensisN/A
Find proteins for Q9IAT9 (Bothrops pauloensis)
Go to UniProtKB:  Q9IAT9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.186 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.670α = 90.00
b = 57.670β = 90.00
c = 130.130γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance