1XXS

Structural insights for fatty acid binding in a Lys49 phospholipase A2: crystal structure of myotoxin II from Bothrops moojeni complexed with stearic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights for fatty acid binding in a Lys49-phospholipase A(2): crystal structure of myotoxin II from Bothrops moojeni complexed with stearic acid

Watanabe, L.Soares, A.M.Ward, R.J.Fontes, M.R.Arni, R.K.

(2005) Biochimie 87: 161-167

  • DOI: 10.1016/j.biochi.2004.11.005

  • PubMed Abstract: 
  • The crystal structure of dimeric Lys49-phospholipase A2 myotoxin-II from Bothrops moojeni (MjTX-II) co-crystallized with stearic acid (C(18)H(36)O(2)) has been determined at a resolution of 1.8 A. The electron density maps permitted the unambiguous i ...

    The crystal structure of dimeric Lys49-phospholipase A2 myotoxin-II from Bothrops moojeni (MjTX-II) co-crystallized with stearic acid (C(18)H(36)O(2)) has been determined at a resolution of 1.8 A. The electron density maps permitted the unambiguous inclusion of six stearic acid molecules in the refinement. Two stearic acid molecules could be located in the substrate-binding cleft of each monomer in positions, which favor the interaction of their carboxyl groups with active site residues. The way of binding of stearic acids to this Lys49-PLA(2)s is analogous to phospholipids and transition state analogues to catalytically active PLA(2)s. Two additional stearic acid molecules were located at the dimer interface region, defining a hitherto unidentified acyl-binding site on the protein surface. The strictly conserved Lys122 for Lys49-PLA(2)s may play a fundamental role for stabilization of legend-protein complex. The comparison of MjTX-II/satiric acid complex with other Lys-PLA(2)s structures whose putative fatty acids were located at their active site is also analysed. Molecular details of the stearic acid/protein interactions provide insights to binding in group I/II PLA(2)s, and to the possible interactions of Lys49-PLA(2)s with target membranes.


    Related Citations: 
    • Crystal Structure of miotoxin-II: a myotoxic phospholipase A2 homologue from Bothrops moojeni venom
      de Azevedo Jr., W.F.,Ward, R.J.,Lombardi, F.R.,Giglio, J.R.,Soares, A.M.,Fontes, M.R.M.,Arni, R.K.
      (1997) PROTEIN PEPT.LETT. 4: 329
    • A rapid procedure for the isolation of the Lys-49 myotoxin II from Bothrops moojeni (caissaca) venom: biochemical characterization, crystallization, myotoxic and edematogenic activity
      Soares, A.M.,Rodrigues, V.M.,Homsi-Brandeburgo, M.I.,Toyama, M.H.,Lombardi, F.R.,Arni, R.K.,Giglio, J.R.
      (1998) Toxicon 36: 503
    • Initiating structural studies of Lys49-PLA2 homologues complexed with an anionic detergent, a fatty acid and a natural lipid
      Watanabe, L.,Fontes, M.R.,Soares, A.M.,Giglio, J.R.,Arni, R.K.
      (2003) PROTEIN PEPT.LETT. 10: 525
    • Structural and functional characterization of myotoxin I, a Lys49 phospholipase A(2) homologue from Bothrops moojeni (Caissaca) snake venom
      Soares, A.M.,Andriao-Escarso, S.H.,Angulo, Y.,Lomonte, B.,Gutierrez, J.M.,Marangoni, S.,Toyama, M.H.,Arni, R.K.,Giglio, J.R.
      (2000) Arch.Biochem.Biophys. 373: 7


    Organizational Affiliation

    Departamento de FĂ­sica, IBILCE, UNESP, S. J. do Rio Preto-SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Download SDF File 
Download CCD File 
A, B
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
 Ligand Interaction
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: 1.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.180α = 90.00
b = 88.710β = 90.00
c = 51.090γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance