5P2P

X-RAY STRUCTURE OF PHOSPHOLIPASE A2 COMPLEXED WITH A SUBSTRATE-DERIVED INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor.

Thunnissen, M.M.Ab, E.Kalk, K.H.Drenth, J.Dijkstra, B.W.Kuipers, O.P.Dijkman, R.de Haas, G.H.Verheij, H.M.

(1990) Nature 347: 689-691

  • DOI: 10.1038/347689a0

  • PubMed Abstract: 
  • Phospholipases A2 play a part in a number of physiologically important cellular processes such as inflammation, blood platelet aggregation and acute hypersensitivity. These processes are all initiated by the release of arachidonic acid from cell memb ...

    Phospholipases A2 play a part in a number of physiologically important cellular processes such as inflammation, blood platelet aggregation and acute hypersensitivity. These processes are all initiated by the release of arachidonic acid from cell membranes which is catalysed by intracellular phospholipases A2 and followed by conversion of arachidonic acid to prostaglandins, leukotrienes or thromboxanes. An imbalance in the production of these compounds can lead to chronic inflammatory diseases such as rheumatoid arthritis and asthma. Inhibitors of phospholipase A2 might therefore act to reduce the effects of inflammation, so structural information about the binding of phospholipase A2 to its substrates could be helpful in the design of therapeutic drugs. The three-dimensional structure is not known for any intracellular phospholipase A2, but these enzymes share significant sequence homology with secreted phospholipases, for which some of the structures have been determined. Here we report the structure of a complex between an extracellular phospholipase A2 and a competitively inhibiting substrate analogue, which reveals considerable detail about the interaction and suggests a mechanism for catalysis by this enzyme.


    Related Citations: 
    • 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
    • Structure of Porcine Pancreatic Phospholipase A2 at 2.6 Angstroms Resolution and Comparison with Bovine Phospholipase A2
      Dijkstra, B.W.,Renetseder, R.,Kalk, K.H.,Hol, W.G.J.,Drenth, J.
      (1983) J.Mol.Biol. 168: 163
    • Enhanced Activity and Altered Specificity of Phospholipase A2 by Deletion of a Surface Loop
      Kuipers, O.P.,Thunnissen, M.M.G.M.,Degeus, P.,Dijkstra, B.W.,Drenth, J.,Verheij, H.M.,Dehaas, G.H.
      (1989) Science 244: 82
    • Structure of an Engineered Porcine Phospholipase A2 with Enhanced Activity at 2.1 Angstroms Resolution. Comparison with the Wild-Type Porcine and Crotalus Atrox PhospholipaseA2
      Thunnissen, M.M.G.M.,Kalk, K.H.,Drenth, J.,Dijkstra, B.W.
      (1990) J.Mol.Biol. 216: 425
    • Active Site and Catalytic Mechanism of Phospholipase A2
      Dijkstra, B.W.,Drenth, J.,Kalk, K.H.
      (1981) Nature 289: 604


    Organizational Affiliation

    Laboratory of Chemical Physics, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A, B
119Sus 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 2 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
DHG
Query on DHG

Download SDF File 
Download CCD File 
A, B
PHOSPHONIC ACID 2-DODECANOYLAMINO-HEXYL ESTER PROPYL ESTER
C20 H42 N O6 P
SLLQAGCLXXPCKZ-LJQANCHMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.570α = 90.00
b = 62.440β = 90.00
c = 85.580γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance