1BCI

C2 DOMAIN OF CYTOSOLIC PHOSPHOLIPASE A2, NMR, MINIMIZED AVERAGE STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 75 
  • Conformers Submitted: 
  • Selection Criteria: VIOLATION: NOES<0.3 A, DIHEDRAL ANGLES<3 DEGREES 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure and membrane interactions of the C2 domain of cytosolic phospholipase A2.

Xu, G.Y.McDonagh, T.Yu, H.A.Nalefski, E.A.Clark, J.D.Cumming, D.A.

(1998) J.Mol.Biol. 280: 485-500

  • DOI: 10.1006/jmbi.1998.1874

  • PubMed Abstract: 
  • The amino-terminal, 138 amino acid C2 domain of cytosolic phospholipase A2 (cPLA2-C2) mediates an initial step in the production of lipid mediators of inflammation: the Ca2+-dependent translocation of the enzyme to intracellular membranes with subseq ...

    The amino-terminal, 138 amino acid C2 domain of cytosolic phospholipase A2 (cPLA2-C2) mediates an initial step in the production of lipid mediators of inflammation: the Ca2+-dependent translocation of the enzyme to intracellular membranes with subsequent liberation of arachidonic acid. The high resolution solution structure of this Ca2+-dependent, lipid-binding domain (CaLB) has been determined using heteronuclear three-dimensional NMR spectroscopy. Secondary structure analysis, derived from several sets of spectroscopic data, shows that the domain is composed of eight antiparallel beta-strands with six interconnecting loops that fits the "type II" topology for C2 domains. Using a total of 2370 distance and torsional restraints, the structure was found to be a beta-sandwich in the "Greek key" motif. The solution structure of cPLA2-C2 domain is very similar to the X-ray crystal structure of the C2 domain of phospholipase-C-delta and phylogenetic analysis clarifies the structural role of highly conserved residues. Calorimetric studies further demonstrate that cPLA2-C2 binds two Ca2+ with observed Kds of approximately 2 microM in an entropically assisted process. Moreover, regions on cPLA2-C2 interacting with membranes were identified by 15N-HSQC-spectroscopy of cPLA2-C2 in the presence of low molecular weight lipid micelles. An extended binding site was identified that binds the phosphocholine headgroup in a Ca2+-dependent manner and also interacts with proximal regions of the membrane surface. Based upon these results, a structural model is presented for the mechanism of association of cPLA2 with its membrane substrate.


    Organizational Affiliation

    Small Molecule Drug Discovery, Genetics Institute, 87 Cambridge Park Drive, Cambridge, MA 02140, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOSOLIC PHOSPHOLIPASE A2
A
138Homo sapiensMutation(s): 0 
Gene Names: PLA2G4A (CPLA2, PLA2G4)
Find proteins for P47712 (Homo sapiens)
Go to Gene View: PLA2G4A
Go to UniProtKB:  P47712
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CAΔH: -26 kJ/mol (100) BINDINGDB
CAΔG: -33.2 kJ/mol (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 75 
  • Conformers Submitted: 
  • Selection Criteria: VIOLATION: NOES<0.3 A, DIHEDRAL ANGLES<3 DEGREES 
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-25
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance