4QN9

Structure of human NAPE-PLD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.652 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 

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

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
A, B
393Homo sapiensMutation(s): 0 
Gene Names: NAPEPLD (C7orf18)
EC: 3.1.4.54
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Hydrolases
Protein: 
N-acylphosphatidylethanolamine-hydrolyzing phospholipase D
Find proteins for Q6IQ20 (Homo sapiens)
Go to Gene View: NAPEPLD
Go to UniProtKB:  Q6IQ20
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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

Download SDF File 
Download CCD File 
A, B
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
3-SN-PHOSPHATIDYLETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.652 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 95.099α = 90.00
b = 95.099β = 90.00
c = 444.170γ = 120.00
Software Package:
Software NamePurpose
CCP4refinement
iMOSFLMdata reduction
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Refinement description