3JR8

Crystal Structure of BthTX-II (Asp49-PLA2 from Bothrops jararacussu snake venom) with calcium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural, functional, and bioinformatics studies reveal a new snake venom homologue phospholipase A2 class.

dos Santos, J.I.Cintra-Francischinelli, M.Borges, R.J.Fernandes, C.A.Pizzo, P.Cintra, A.C.Braz, A.S.Soares, A.M.Fontes, M.R.

(2011) Proteins 79: 61-78

  • DOI: 10.1002/prot.22858

  • PubMed Abstract: 
  • Phospholipases A₂ (PLA₂s) are enzymes responsible for membrane disruption through Ca(2+) -dependent hydrolysis of phospholipids. Lys49-PLA₂s are well-characterized homologue PLA₂s that do not show catalytic activity but can exert a pronounced local m ...

    Phospholipases A₂ (PLA₂s) are enzymes responsible for membrane disruption through Ca(2+) -dependent hydrolysis of phospholipids. Lys49-PLA₂s are well-characterized homologue PLA₂s that do not show catalytic activity but can exert a pronounced local myotoxic effect. These homologue PLA₂s were first believed to present residual catalytic activity but experiments with a recombinant toxin show they are incapable of catalysis. Herein, we present a new homologue Asp49-PLA₂ (BthTX-II) that is also able to exert muscle damage. This toxin was isolated in 1992 and characterized as presenting very low catalytic activity. Interestingly, this myotoxic homologue Asp49-PLA₂ conserves all the residues responsible for Ca(2+) coordination and of the catalytic network, features thought to be fundamental for PLA₂ enzymatic activity. Previous crystallographic studies of apo BthTX-II suggested this toxin could be catalytically inactive since a distortion in the calcium binding loop was observed. In this article, we show BthTX-II is not catalytic based on an in vitro cell viability assay and time-lapse experiments on C2C12 myotube cell cultures, X-ray crystallography and phylogenetic studies. Cell culture experiments show that BthTX-II is devoid of catalytic activity, as already observed for Lys49-PLA₂s. Crystallographic studies of the complex BthTX-II/Ca(2+) show that the distortion of the calcium binding loop is still present and impairs ion coordination even though Ca(2+) are found interacting with other regions of the protein. Phylogenetic studies demonstrate that BthTX-II is more phylogenetically related to Lys49-PLA₂s than to other Asp49-PLA₂s, thus allowing Crotalinae subfamily PLA₂s to be classified into two main branches: a catalytic and a myotoxic one.


    Organizational Affiliation

    Departamento de Física e Biofísica, Instituto de Biociências, UNESP - Univ Estadual Paulista, Botucatu-SP and Instituto Nacional de Ciência e Tecnologia em Toxinas, CNPq, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospholipase A2 bothropstoxin-2
A, B
122Bothrops jararacussuMutation(s): 0 
EC: 3.1.1.4
Find proteins for P45881 (Bothrops jararacussu)
Go to UniProtKB:  P45881
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.236α = 90.00
b = 100.879β = 126.00
c = 47.166γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-06-26
    Type: Database references