6B84

Crystal structure of Myotoxin II from Bothrops moojeni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.997 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural evidence for a fatty acid-independent myotoxic mechanism for a phospholipase A2-like toxin.

Salvador, G.H.M.Dos Santos, J.I.Borges, R.J.Fontes, M.R.M.

(2018) Biochim Biophys Acta Proteins Proteom 1866: 473-481

  • DOI: 10.1016/j.bbapap.2017.12.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The myotoxic mechanism for PLA <sub>2 </sub>-like toxins has been proposed recently to be initiated by an allosteric change induced by a fatty acid binding to the protein, leading to the alignment of the membrane docking site (MDoS) and membrane disr ...

    The myotoxic mechanism for PLA 2 -like toxins has been proposed recently to be initiated by an allosteric change induced by a fatty acid binding to the protein, leading to the alignment of the membrane docking site (MDoS) and membrane disrupting site (MDiS). Previous structural studies performed by us demonstrated that MjTX-II, a PLA 2 -like toxin isolated from Bothrops moojeni, presents a different mode of ligand-interaction caused by natural amino acid substitutions and an insertion. Herein, we present four crystal structures of MjTX-II, in its apo state and complexed with fatty acids of different lengths. Analyses of these structures revealed slightly different oligomeric conformations but with both MDoSs in an arrangement that resembles an active-state PLA 2 -like structure. To explore the structural transitions between apo protein and fatty-acid complexes, we performed Normal Mode Molecular Dynamics simulations, revealing that oligomeric conformations of MjTX-II/fatty acid complexes may be reached in solution by the apo structure. Similar simulations with typical PLA 2 -like structures demonstrated that this transition is not possible without the presence of fatty acids. Thus, we hypothesize that MjTX-II does not require fatty acids to be active, although these ligands may eventually help in its stabilization by the formation of hydrogen bonds. Therefore, these results complement previous findings for MjTX-II and help us understand its particular ligand-binding properties and, more importantly, its particular mechanism of action, with a possible impact on the design of structure-based inhibitors for PLA 2 -like toxins in general.


    Organizational Affiliation

    Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.,Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil. Electronic address: fontes@ibb.unesp.br.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Basic phospholipase A2 homolog 2
B, A
122Bothrops moojeniMutation(s): 0 
Find proteins for Q9I834 (Bothrops moojeni)
Go to UniProtKB:  Q9I834
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.997 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.848α = 90.00
b = 63.848β = 90.00
c = 126.366γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
Cootmodel building
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research FoundationBrazil2015/24167-7

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Author supporting evidence, Data collection