6IEJ

The C2 domain of cytosolic phospholipase A2 alpha bound to phosphatidylcholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.206 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of phosphatidylcholine recognition by the C2-domain of cytosolic phospholipase A2alpha.

Hirano, Y.Gao, Y.G.Stephenson, D.J.Vu, N.T.Malinina, L.Simanshu, D.K.Chalfant, C.E.Patel, D.J.Brown, R.E.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.44760

  • PubMed Abstract: 
  • Ca <sup>2+ </sup>-stimulated translocation of cytosolic phospholipase A <sub>2 </sub>α (cPLA <sub>2 </sub>α) to the Golgi induces arachidonic acid production, the rate-limiting step in pro-inflammatory eicosanoid synthesis. Structural insights into t ...

    Ca 2+ -stimulated translocation of cytosolic phospholipase A 2 α (cPLA 2 α) to the Golgi induces arachidonic acid production, the rate-limiting step in pro-inflammatory eicosanoid synthesis. Structural insights into the cPLA 2 α preference for phosphatidylcholine (PC)-enriched membranes have remained elusive. Here, we report cPLA 2 α C2-domain structure (2.2Å resolution) containing bound 1,2-dihexanoyl- sn -glycero-3-phosphocholine (DHPC) and Ca 2+ ions. Two Ca 2+ are complexed at locations previously reported for lipid-free C2-domain. One of these Ca 2+ along with a third Ca 2+ bridge the C2-domain to the DHPC phosphate group, which also interacts with Asn65. Tyr96 plays a key role in lipid headgroup recognition via cation-π interaction with the PC trimethylammonium group. Mutagenesis analyses confirm Tyr96 and Asn65 function in PC binding selectivity by C2-domain and regulation of cPLA 2 α activity. The differing DHPC-binding mode of cPLA 2 α C2-domain, compared to phosphatidylserine or phosphatidylinositol 4,5-bisphosphate binding by other C2-domains, expands and deepens knowledge of lipid-binding mechanisms mediated by C2-domains.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, United States.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, United States.,Hormel Institute, University of Minnesota, Austin, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytosolic phospholipase A2
A, B, C
127Gallus gallusMutation(s): 0 
Gene Names: PLA2G4A (CPLA2, PLA2G4)
Membrane protein
mpstruc
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Hydrolases
Protein: 
C2 domain of cytosolic phospholipase A2α bound to phosphatidylcholine
Find proteins for P49147 (Gallus gallus)
Go to Gene View: PLA2G4A
Go to UniProtKB:  P49147
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HXG
Query on HXG

Download SDF File 
Download CCD File 
A, B, C
1,2-dihexanoyl-sn-glycero-3-phosphocholine
(4R,7R)-7-(hexanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphapentadecan-1-aminium 4-oxide
C20 H41 N O8 P
DVZARZBAWHITHR-GOSISDBHSA-O
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.206 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.294α = 90.00
b = 187.388β = 90.00
c = 68.754γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesHL125353

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release