1M8R

Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 7.4)

Summary for 1M8R

• Entry DOI: 10.2210/pdb1m8r/pdb
• Related: 1BK9 1M8S 1PSJ
• Descriptor: phospholipase A2, CADMIUM ION, 1,4-BUTANEDIOL, ... (4 entities in total)
• Functional Keywords: phopholipase a2-metal cation complex, three alpha, two beta, hydrolase
• Biological source: Gloydius halys (halys viper)
• Cellular location: Secreted: P14418
• Total number of polymer chains: 1
• Total formula weight: 14249.34

Authors

Xu, S.,Gu, L.,Zhou, Y.,Lin, Z. (deposition date: 2002-07-25, release date: 2003-02-11, Last modification date: 2024-10-09)

Primary citation

Xu, S.,Gu, L.,Jiang, T.,Zhou, Y.,Lin, Z.
Structures of cadmium-binding acidic phospholipase A(2) from the venom of Agkistrodon halys Pallas at 1.9A resolutio
Biochem.Biophys.Res.Commun., 300:271-277, 2003

PubMed Abstract: Phospholipase A(2) coordinates Ca(2+) ion through three carbonyl oxygen atoms of residues 28, 30, and 32, two carboxyl oxygen atoms of residue Asp49, and two (or one) water molecules, forming seven (or six) coordinate geometry of Ca(2+) ligands. Two crystal structures of cadmium-binding acidic phospholipase A(2) from the venom of Agkistrodon halys Pallas (i.e., Agkistrodon blomhoffii brevicaudus) at different pH values (5.9 and 7.4) were determined to 1.9A resolution by the isomorphous difference Fourier method. The well-refined structures revealed that a Cd(2+) ion occupied the position expected for a Ca(2+) ion, and that the substitution of Cd(2+) for Ca(2+) resulted in detectable changes in the metal-binding region: one of the carboxyl oxygen atoms from residue Asp49 was farther from the metal ion while the other one was closer and there were no water molecules coordinating to the metal ion. Thus the Cd(2+)-binding region appears to have four coordinating oxygen ligands. The cadmium binding to the enzyme induced no other significant conformational change in the enzyme molecule elsewhere. The mechanism for divalent cadmium cation to support substrate binding but not catalysis is discussed.

PubMed: 12504079
DOI: 10.1016/S0006-291X(02)02833-4

Experimental method

X-RAY DIFFRACTION (1.9 Å)