PDBsum entry 2ph4

Toxin

PDB id: 2ph4

Contents

Protein chains

121 a.a. *

Ligands

SO4 ×5

PEG ×2

Waters ×235

* Residue conservation analysis

PDB id:

2ph4

Name:

Toxin

Title:

Crystal structure of a novel arg49 phospholipase a2 homologue from zhaoermia mangshanensis venom

Structure:

Zhaoermiatoxin. Chain: a, b. Synonym: phospholipase a2 homolog

Source:

Zhaoermia mangshanensis. Organism_taxid: 242058. Secretion: venom

Resolution:

2.05Å R-factor: 0.217 R-free: 0.289

Authors:

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

Key ref:

M.T.Murakami et al. (2008). 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. Toxicon, 51, 723-735. PubMed id: 18295812 DOI: 10.1016/j.toxicon.2007.11.018

Date:

10-Apr-07 Release date: 18-Mar-08

Protein chains

P84776  (PA2H_PROMB) -  Basic phospholipase A2 homolog zhaoermiatoxin from Protobothrops mangshanensis

Seq: 121 a.a.

Struc: 121 a.a.

DOI no: 10.1016/j.toxicon.2007.11.018

Toxicon 51:723-735 (2008)

PubMed id: 18295812

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.

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

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.