1PC9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 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

  • DOI: 10.1016/j.bbrc.2003.10.047
  • Primary Citation of Related Structures:  
    1PA0, 1PC9

  • 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, due to a D49K mutation, is still highly myonecrotic ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BnSP-6A, B121Bothrops pauloensisMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for Q9IAT9 (Bothrops pauloensis)
Explore Q9IAT9 
Go to UniProtKB:  Q9IAT9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.186 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.67α = 90
b = 57.67β = 90
c = 130.13γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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