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 

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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-acylphosphatidylethanolamines (NAPEs) and include agonists for G protein-coupled receptors (e ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase DA, B393Homo sapiensMutation(s): 0 
Gene Names: C7orf18, NAPEPLD
EC: 3.1.4.54
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IQ20 (Homo sapiens)
Explore Q6IQ20 
Go to UniProtKB:  Q6IQ20
PHAROS:  Q6IQ20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IQ20
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 Ideal Coordinates CCD File 
E [auth A],
Q [auth B]		1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N		 Ligand Interaction
DXC
Query on DXC
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
V [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
O [auth B],
P [auth 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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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