Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.50 kDa 
• Atom Count: 2261 
• Modelled Residue Count: 242 
• Deposited Residue Count: 242 
• Unique protein chains: 1

1PA0

CRYSTAL STRUCTURE OF BNSP-7, A LYS49-PHOSPHOLIPASE A2

• PDB DOI: 10.2210/pdb1PA0/pdb

• Classification: HYDROLASE
• Organism(s): Bothrops pauloensis
• Mutation(s): No 


• Deposited: 2003-05-13 Released: 2004-07-27 
• Deposition Author(s): Magro, A.J., Soares, A.M., Giglio, J.R., Fontes, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 

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.

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

• PubMed: 14623331 
• 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. 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.

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Related Citations: 

• Crystallization and preliminary X-ray diffraction analysis of a myotoxic phospholipase A2 homologue from Bothrops neuwiedi pauloensis venom
  Fontes, M.R., Soares, A.M., Rodrigues, V.M., Fernandes, A.C., Da Silva, R.J., Giglio, J.R.
  (1999) Biochim Biophys Acta 1432: 393

• Structural and Function Characterization of BnSP-7, a Lys49 Myotoxic Phospholipase A2 Homologue from Bothrops neuwiedi Venom
  Soares, A.M., Guerra-Sa, R., Borja-Oliveira, C.R., Rodrigues, V.M., Rodrigues-Simioni, L., Rodrigues, V., Fontes, M.R., Lomonte, B., Gutirrez, J.M., Giglio, J.R.
  (2000) Arch Biochem Biophys 378: 201

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myotoxic phospholipase A2-like	A, B	121	Bothrops pauloensis	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for Q9IAT9 (Bothrops pauloensis) Explore Q9IAT9  Go to UniProtKB:  Q9IAT9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.33	α = 90
b = 57.33	β = 90
c = 130.86	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-13 
• Released Date: 2004-07-27 
Deposition Author(s): Magro, A.J., Soares, A.M., Giglio, J.R., Fontes, M.R.

Revision History  

• Version 1.0: 2004-07-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance