6DY0

Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) covalently bound to beta-lactam inhibitor ARN726, in presence of Triton X-100


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Molecular mechanism of activation of the immunoregulatory amidase NAAA.

Gorelik, A.Gebai, A.Illes, K.Piomelli, D.Nagar, B.

(2018) Proc Natl Acad Sci U S A 115: E10032-E10040

  • DOI: 10.1073/pnas.1811759115
  • Primary Citation of Related Structures:  
    6DXZ, 6DY3, 6DXW, 6DXY, 6DXX, 6DY0, 6DY2, 6DY1

  • PubMed Abstract: 
  • Palmitoylethanolamide is a bioactive lipid that strongly alleviates pain and inflammation in animal models and in humans. Its signaling activity is terminated through degradation by N -acylethanolamine acid amidase (NAAA), a cysteine hydrolase expressed at high levels in immune cells ...

    Palmitoylethanolamide is a bioactive lipid that strongly alleviates pain and inflammation in animal models and in humans. Its signaling activity is terminated through degradation by N -acylethanolamine acid amidase (NAAA), a cysteine hydrolase expressed at high levels in immune cells. Pharmacological inhibitors of NAAA activity exert profound analgesic and antiinflammatory effects in rodent models, pointing to this protein as a potential target for therapeutic drug discovery. To facilitate these efforts and to better understand the molecular mechanism of action of NAAA, we determined crystal structures of this enzyme in various activation states and in complex with several ligands, including both a covalent and a reversible inhibitor. Self-proteolysis exposes the otherwise buried active site of NAAA to allow catalysis. Formation of a stable substrate- or inhibitor-binding site appears to be conformationally coupled to the interaction of a pair of hydrophobic helices in the enzyme with lipid membranes, resulting in the creation of a linear hydrophobic cavity near the active site that accommodates the ligand's acyl chain.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, H3G0B1, Canada; bhushan.nagar@mcgill.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acylethanolamine acid amidase alpha-subunitA107Oryctolagus cuniculusMutation(s): 0 
Gene Names: NAAA
EC: 3.5.1.60 (PDB Primary Data), 3.5.1.23 (UniProt)
UniProt
Find proteins for G1T7U7 (Oryctolagus cuniculus)
Explore G1T7U7 
Go to UniProtKB:  G1T7U7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-acylethanolamine acid amidase beta-subunitB232Oryctolagus cuniculusMutation(s): 0 
Gene Names: NAAA
EC: 3.5.1.60 (PDB Primary Data), 3.5.1.23 (UniProt)
UniProt
Find proteins for G1T7U7 (Oryctolagus cuniculus)
Explore G1T7U7 
Go to UniProtKB:  G1T7U7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HJA (Subject of Investigation/LOI)
Query on HJA

Download Ideal Coordinates CCD File 
S [auth B](2S)-3-amino-2-{[(4-cyclohexylbutoxy)carbonyl]amino}propanethioic S-acid
C14 H26 N2 O3 S
PRQLPRBNQTXHJV-LBPRGKRZSA-N
 Ligand Interaction
TON (Subject of Investigation/LOI)
Query on TON

Download Ideal Coordinates CCD File 
I [auth A], J [auth A]2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL
C18 H30 O3
LBCZOTMMGHGTPH-UHFFFAOYSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  K [auth B],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.199 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.871α = 90
b = 157.871β = 90
c = 157.871γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-133535

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.4: 2019-04-17
    Changes: Data collection, Structure summary
  • Version 1.5: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary