1P2P

STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 AT 2.6 ANGSTROMS RESOLUTION AND COMPARISON WITH BOVINE PHOSPHOLIPASE A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of porcine pancreatic phospholipase A2 at 2.6 A resolution and comparison with bovine phospholipase A2.

Dijkstra, B.W.Renetseder, R.Kalk, K.H.Hol, W.G.Drenth, J.

(1983) J.Mol.Biol. 168: 163-179


  • PubMed Abstract: 
  • The previously published three-dimensional structure of porcine pancreatic prophospholipase A2 at 3 A resolution was found to be incompatible with the structures of bovine phospholipase A2 and bovine prophospholipase A2. This was unexpected because o ...

    The previously published three-dimensional structure of porcine pancreatic prophospholipase A2 at 3 A resolution was found to be incompatible with the structures of bovine phospholipase A2 and bovine prophospholipase A2. This was unexpected because of the very homologous amino acid sequences of these enzymes. Therefore, the crystal structure of the porcine enzyme was redetermined using molecular replacement methods with bovine phospholipase as the parent model. The structure was crystallographically refined at 2.6 A resolution by fast Fourier transform and restrained least-squares procedures to an R-factor of 0.241. The crystals appeared to contain phospholipase A2 and not prophospholipase A2. Apparently the protein is slowly converted under the crystallization conditions employed. Our investigation shows that, in contrast to the previous report, the three-dimensional structure of porcine phospholipase A2 is very similar to that of bovine phospholipase A2, including the active site. Smaller differences were observed in some residues involved in the binding of aggregated substrates. However, an appreciable conformational difference is in the loop 59 to 70, where a single substitution at position 63 (bovine Val leads to porcine Phe) causes a complete rearrangement of the peptide chain. In addition to the calcium ion in the active site, a second calcium ion is present in the crystals; this is located on a crystallographic 2-fold axis and stabilizes the interaction between two neighbouring molecules.


    Related Citations: 
    • Active Site and Catalytic Mechanism of Phospholipase A2
      Dijkstra, B.W.,Drenth, J.,Kalk, K.H.
      (1981) Nature 289: 604
    • Structure of Bovine Pancreatic Phospholipase A2 at 1.7 Angstroms Resolution
      Dijkstra, B.W.,Kalk, K.H.,Hol, W.G.J.,Drenth, J.
      (1981) J.Mol.Biol. 147: 97
    • The Structure of Bovine Pancreatic Prophospholipase A2 at 3.0 Angstroms Resolution
      Dijkstra, B.W.,Vannes, G.J.H.,Kalk, K.H.,Brandenburg, N.P.,Hol, W.G.J.,Drenth, J.
      (1982) Acta Crystallogr.,Sect.B 38: 793
    • Three-Dimensional Structure and Disulfide Bond Connections in Bovine Pancreatic Phospholipase A2
      Dijkstra, B.W.,Drenth, J.,Kalk, K.H.,Vandermaelen, P.J.
      (1978) J.Mol.Biol. 124: 53



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A
124Sus scrofaGene Names: PLA2G1B
EC: 3.1.1.4
Find proteins for P00592 (Sus scrofa)
Go to Gene View: PLA2G1B
Go to UniProtKB:  P00592
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.241 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.820α = 90.00
b = 69.820β = 90.00
c = 67.660γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1983-09-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other