2PH4

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

Summary for 2PH4

• Entry DOI: 10.2210/pdb2ph4/pdb
• Descriptor: Zhaoermiatoxin, SULFATE ION, DI(HYDROXYETHYL)ETHER, ... (4 entities in total)
• Functional Keywords: snake venom, arg49, phospholipase a2, myotoxin, toxin
• Biological source: Zhaoermia mangshanensis
• Cellular location: Secreted: P84776
• Total number of polymer chains: 2
• Total formula weight: 28713.48

Authors

Murakami, M.T.,Kuch, U.,Mebs, D.,Arni, R.K. (deposition date: 2007-04-10, release date: 2008-03-18, Last modification date: 2024-10-16)

Primary citation

Murakami, M.T.,Kuch, U.,Betzel, C.,Mebs, D.,Arni, R.K.
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.
Toxicon, 51:723-735, 2008

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. 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.

PubMed: 18295812
DOI: 10.1016/j.toxicon.2007.11.018

Experimental method

X-RAY DIFFRACTION (2.05 Å)