PDBsum entry 2ph4

Toxin

PDB id: 2ph4

Contents

Protein chains

121 a.a.

Ligands

SO4 ×5

PEG ×2

Waters ×235

References listed in PDB file

Key reference

• Title: Crystal structure of a novel myotoxic arg49 phospholipase a2 homolog (zhaoermiatoxin) from zhaoermia mangshanensis snake venom: insights into arg49 coordination and the role of lys122 in the polarization of the c-Terminus.
• Authors: M.T.Murakami, U.Kuch, C.Betzel, D.Mebs, R.K.Arni.
• Ref.: Toxicon, 2008, 51, 723-735. [DOI no: 10.1016/j.toxicon.2007.11.018]
• PubMed id: 18295812

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.