4X97

Crystal structure of Lysosomal Phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (MAFP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and function of lysosomal phospholipase A2 and lecithin:cholesterol acyltransferase.

Glukhova, A.Hinkovska-Galcheva, V.Kelly, R.Abe, A.Shayman, J.A.Tesmer, J.J.

(2015) Nat Commun 6: 6250-6250

  • DOI: 10.1038/ncomms7250
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lysosomal phospholipase A2 (LPLA2) and lecithin:cholesterol acyltransferase (LCAT) belong to a structurally uncharacterized family of key lipid-metabolizing enzymes responsible for lung surfactant catabolism and for reverse cholesterol transport, res ...

    Lysosomal phospholipase A2 (LPLA2) and lecithin:cholesterol acyltransferase (LCAT) belong to a structurally uncharacterized family of key lipid-metabolizing enzymes responsible for lung surfactant catabolism and for reverse cholesterol transport, respectively. Whereas LPLA2 is predicted to underlie the development of drug-induced phospholipidosis, somatic mutations in LCAT cause fish eye disease and familial LCAT deficiency. Here we describe several high-resolution crystal structures of human LPLA2 and a low-resolution structure of LCAT that confirms its close structural relationship to LPLA2. Insertions in the α/β hydrolase core of LPLA2 form domains that are responsible for membrane interaction and binding the acyl chains and head groups of phospholipid substrates. The LCAT structure suggests the molecular basis underlying human disease for most of the known LCAT missense mutations, and paves the way for rational development of new therapeutics to treat LCAT deficiency, atherosclerosis and acute coronary syndrome.


    Organizational Affiliation

    1] Life Sciences Institute and the Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA [2] Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Group XV phospholipase A2
A, B, C, D
380Homo sapiensMutation(s): 0 
Gene Names: PLA2G15 (LYPLA3)
EC: 2.3.1.-
Find proteins for Q8NCC3 (Homo sapiens)
Go to Gene View: PLA2G15
Go to UniProtKB:  Q8NCC3
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B, C, D
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAY
Query on MAY

Download SDF File 
Download CCD File 
A, B, C, D
METHYL ARACHIDONYL FLUOROPHOSPHONATE
MAFP
C21 H36 F O2 P
KWKZCGMJGHHOKJ-WTIHWRCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.179 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 69.147α = 88.85
b = 85.495β = 70.87
c = 88.852γ = 79.74
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Cootmodel building
SCALEPACKdata scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

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 StatesHL086865

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-18
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.3: 2017-11-22
    Type: Refinement description