2PH4

Crystal structure of a novel Arg49 phospholipase A2 homologue from Zhaoermia mangshanensis venom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a novel myotoxic Arg49 phospholipase A(2) homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: Insights into Arg49 coordination and the role of Lys122 in the polarization of the C-terminus.

Murakami, M.T.Kuch, U.Betzel, C.Mebs, D.Arni, R.K.

(2008) Toxicon 51: 723-735

  • DOI: 10.1016/j.toxicon.2007.11.018
  • Primary Citation of Related Structures:  
    2PH4

  • PubMed Abstract: 
  • The venom of Zhaoermia mangshanensis, encountered solely in Mt Mang in China's Hunan Province, exhibits coagulant, phosphodiesterase, l-amino acid oxidase, kallikrein, phospholipase A2 and myotoxic activities. The catalytically inactive PLA2 homolog referred to as zhaoermiatoxin is highly myotoxic and displays high myonecrotic and edema activities ...

    The venom of Zhaoermia mangshanensis, encountered solely in Mt Mang in China's Hunan Province, exhibits coagulant, phosphodiesterase, l-amino acid oxidase, kallikrein, phospholipase A2 and myotoxic activities. The catalytically inactive PLA2 homolog referred to as zhaoermiatoxin is highly myotoxic and displays high myonecrotic and edema activities. Zhaoermiatoxin possesses a molecular weight of 13,972Da, consists of 121 amino-acid residues cross-linked by seven disulfide bridges and shares high sequence homology with Lys49-PLA2s from the distantly related Asian pitvipers. However, zhaoermiatoxin possesses an arginine residue at position 49 instead of a lysine, thereby suggesting a secondary Lys49-->Arg substitution which results in a catalytically inactive protein. We have determined the first crystal structure of zhaoermiatoxin, an Arg49-PLA2, from Zhaoermia mangshanensis venom at 2.05 angstroms resolution, which represents a novel member of phospholipase A2 family. In this structure, unlike the Lys49 PLA2s, the C-terminus is well ordered and an unexpected non-polarized state of the putative calcium-binding loop due to the flip of Lys122 towards the bulk solvent is observed. The orientation of the Arg-49 side chain results in a similar binding mode to that observed in the Lys49 PLA2s; however, the guadinidium group is tri-coordinated by carbonyl oxygen atoms of the putative calcium-binding loop, whereas the Nzeta atom of lysine is tetra-coordinated as a result of the different conformation adopted by the putative calcium-binding loop.


    Organizational Affiliation

    Center for Structural & Molecular Biology, Department of Physics, IBILCE/UNESP, R. Cristovao Colombo 2265, São José do Rio Preto, São Paulo CEP 15054-000, Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ZhaoermiatoxinA, B121Protobothrops mangshanensisMutation(s): 0 
UniProt
Find proteins for P84776 (Protobothrops mangshanensis)
Explore P84776 
Go to UniProtKB:  P84776
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.217 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.933α = 90
b = 72.933β = 90
c = 93.938γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance