PDBsum entry 1m8s

Hydrolase

PDB id: 1m8s

Contents

Protein chain

124 a.a. *

Ligands

BU1 ×2

Metals

_CD

Waters ×110

* Residue conservation analysis

PDB id:

1m8s

Name:

Hydrolase

Title:

Crystal structures of cadmium-binding acidic phospholipase a2 from the venom of agkistrodon halys pallas at 1.9 resolution (crystal grown at ph 5.9)

Structure:

Phospholipase a2. Chain: a. Ec: 3.1.1.4

Source:

Gloydius halys. Halys viper. Organism_taxid: 8714. Secretion: venom

Resolution:

1.90Å R-factor: 0.202 R-free: 0.209

Authors:

S.Xu,L.Gu,Y.Zhou,Z.Lin

Key ref:

S.Xu et al. (2003). Structures of cadmium-binding acidic phospholipase A2 from the venom of Agkistrodon halys Pallas at 1.9A resolution. Biochem Biophys Res Commun, 300, 271-277. PubMed id: 12504079 DOI: 10.1016/S0006-291X(02)02833-4

Date:

25-Jul-02 Release date: 11-Feb-03

Protein chain

O42191  (PA2A7_GLOHA) -  Acidic phospholipase A2 A from Gloydius halys

Seq: 124 a.a.

Struc: 124 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.1.4 - phospholipase A2.
• Reaction: a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3- phosphocholine + a fatty acid + H⁺
• Cofactor: Ca(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0006-291X(02)02833-4

Biochem Biophys Res Commun 300:271-277 (2003)

PubMed id: 12504079

Structures of cadmium-binding acidic phospholipase A2 from the venom of Agkistrodon halys Pallas at 1.9A resolution.

S.Xu, L.Gu, T.Jiang, Y.Zhou, Z.Lin.

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.