PDBsum entry: 1jia

Phospholipase

PDB id: 1jia

Contents

Protein chains

122 a.a. *

Metals

_CA ×2

Waters ×190

* Residue conservation analysis

PDB id:

1jia

Name:

Phospholipase

Title:

Structure of a basic phospholipase a2 from agkistrodon halys pallas at 2.13a resolution

Structure:

Phospholipase a2. Chain: a, b. Ec: 3.1.1.4

Source:

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

Resolution:

2.13Å R-factor: 0.152 R-free: 0.255

Authors:

K.Zhao,Z.Lin

Key ref:

K.Zhao et al. (1998). Structure of a basic phospholipase A2 from Agkistrodon halys Pallas at 2.13 A resolution. Acta Crystallogr D Biol Crystallogr, 54, 510-521. PubMed id: 9761847 DOI: 10.1107/S0907444997013644

Date:

09-Jun-97 Release date: 10-Jun-98

Protein chains

O42187  (PA24_GLOHA) -  Phospholipase A2 B

Seq: 138 a.a.

Struc: 122 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.1.4 - Phospholipase A(2).
• Reaction: Phosphatidylcholine + H₂O = 1-acylglycerophosphocholine + a carboxylate
• Cofactor: Calcium

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

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biological process: lipid catabolic process (3 terms)
• Biochemical function: hydrolase activity (4 terms)

reference

DOI no: 10.1107/S0907444997013644

Acta Crystallogr D Biol Crystallogr 54:510-521 (1998)

PubMed id: 9761847

Structure of a basic phospholipase A2 from Agkistrodon halys Pallas at 2.13 A resolution.

K.Zhao, S.Song, Z.Lin, Y.Zhou.

ABSTRACT

The basic phospholipase A2 isolated from the venom of Agkistrodon halys Pallas (Agkistrodon blomhoffii Brevicaudus) is a hemolytic toxin and one of the few PLA2's capable of hydrolyzing the phospholipids of E. coli membranes in the presence of a bactericidal/permeability-increasing protein (BPI) of neutrophils. The crystal structure has been determined and refined at 2.13 A to an R factor of 16.5% (F > 3sigma) with excellent stereochemistry. A superposition of the two molecules in the asymmetric unit gives an r. m.s. deviation of 0.326 A for all Calpha atoms. The refined structure allowed a detailed comparison with other PLA2 species of known structures. The overall architecture is similar to those of other PLA2's with a few significant differences. One of which is in the region connecting the N-terminal helix and the Ca2+-binding loop. Unexpectedly, the conformation of the peptide plane Cys29-Gly30 in the Ca2+-binding loop is very different to that of other PLA2's. The amide NH of Gly30 does not point toward the proposed site for stabilization of the tetrahedral intermediate oxyanion of the substrate analogue. The structure includes four residues which occur less frequently in other PLA2's. His1, Arg6 and Trp70 located at the interfacial recognition site may play an important role in the interaction with aggregated substrates, while Trp77 contributes to the hydrophobic interactions between the beta-wing and the main body of the molecule. This structure analysis reveals that two clusters of basic residues are located at or near the interfacial recognition site, forming an asymmetric positively charge distribution. In contrast to the acidic isoform, the present enzyme is a dimer in the crystalline state. The special phospholipid hydrolysis behaviors are discussed in the light of the structure determined.

Selected figure(s)

Figure 6.
Fig. 6. The amino-acid sequences of the basic and the acidic PLA2 from

Figure 9.
Fig. 9. Stereoscopic comparison of

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1998, 54, 510-521) copyright 1998.

Figures were selected by an automated process.