1JIA

STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS AT 2.13A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(1998) Acta Crystallogr.,Sect.D 54: 510-521


  • PubMed 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 bact ...

    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.


    Related Citations: 
    • Preliminary Crystallographic Studies of a Basic Phospholipase A2 from the Venom of Agkistrodon Halys Pallas
      Zhao, K.,Song, S.,Lin, Z.,Zhou, Y.
      (1997) Shengwu Huaxue Zazhi 13: 765


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A, B
122Gloydius halysEC: 3.1.1.4
Find proteins for O42187 (Gloydius halys)
Go to UniProtKB:  O42187
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 97.130α = 90.00
b = 103.690β = 90.00
c = 23.270γ = 90.00
Software Package:
Software NamePurpose
XENGENdata scaling
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
XENGENdata reduction
XENGENdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-06-09 
  • Released Date: 1998-06-10 
  • Deposition Author(s): Zhao, K., Lin, Z.

Revision History 

  • Version 1.0: 1998-06-10
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance