4QN9

Structure of human NAPE-PLD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of human N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: regulation of fatty acid ethanolamide biosynthesis by bile acids.

Magotti, P.Bauer, I.Igarashi, M.Babagoli, M.Marotta, R.Piomelli, D.Garau, G.

(2015) Structure 23: 598-604

  • DOI: 10.1016/j.str.2014.12.018
  • Primary Citation of Related Structures:  
    4QN9

  • PubMed Abstract: 
  • The fatty acid ethanolamides (FAEs) are lipid mediators present in all organisms and involved in highly conserved biological functions, such as innate immunity, energy balance, and stress control. They are produced from membrane N-acylphosphatidyleth ...

    The fatty acid ethanolamides (FAEs) are lipid mediators present in all organisms and involved in highly conserved biological functions, such as innate immunity, energy balance, and stress control. They are produced from membrane N-acylphosphatidylethanolamines (NAPEs) and include agonists for G protein-coupled receptors (e.g., cannabinoid receptors) and nuclear receptors (e.g., PPAR-α). Here, we report the crystal structure of human NAPE-hydrolyzing phospholipase D (NAPE-PLD) at 2.65 Å resolution, a membrane enzyme that catalyzes FAE formation in mammals. NAPE-PLD forms homodimers partly separated by an internal ∼ 9-Å-wide channel and uniquely adapted to associate with phospholipids. A hydrophobic cavity provides an entryway for NAPE into the active site, where a binuclear Zn(2+) center orchestrates its hydrolysis. Bile acids bind with high affinity to selective pockets in this cavity, enhancing dimer assembly and enabling catalysis. These elements offer multiple targets for the design of small-molecule NAPE-PLD modulators with potential applications in inflammation and metabolic disorders.


    Organizational Affiliation

    Department of Drug Discovery and Development, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy. Electronic address: gianpiero.garau@iit.it.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase DAB393Homo sapiensMutation(s): 0 
Gene Names: C7orf18NAPEPLD
EC: 3.1.4.54
Membrane protein
Mpstruc
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Hydrolases
Protein: 
N-acylphosphatidylethanolamine-hydrolyzing phospholipase D
Find proteins for Q6IQ20 (Homo sapiens)
Explore Q6IQ20 
Go to UniProtKB:  Q6IQ20
NIH Common Fund Data Resources
PHAROS  Q6IQ20
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download CCD File 
A, B
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
DXC
Query on DXC

Download CCD File 
A, B
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.099α = 90
b = 95.099β = 90
c = 444.17γ = 120
Software Package:
Software NamePurpose
CCP4refinement
MOLREPphasing
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-06-17 
  • Released Date: 2015-06-17 
  • Deposition Author(s): Garau, G.

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description