6DXY

Murine N-acylethanolamine-hydrolyzing acid amidase (NAAA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.8 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: https://doi.org/10.1073/pnas.1811759115
  • Primary Citation of Related Structures:  
    6DXW, 6DXX, 6DXY, 6DXZ, 6DY0, 6DY1, 6DY2, 6DY3

  • 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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acylethanolamine-hydrolyzing acid amidase subunit alpha
A, C
107Mus musculusMutation(s): 0 
Gene Names: NaaaAsahl
EC: 3.5.1.60
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D7V9 (Mus musculus)
Explore Q9D7V9 
Go to UniProtKB:  Q9D7V9
IMPC:  MGI:1914361
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D7V9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-acylethanolamine-hydrolyzing acid amidase subunit beta
B, D
232Mus musculusMutation(s): 0 
Gene Names: NaaaAsahl
EC: 3.5.1.60
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D7V9 (Mus musculus)
Explore Q9D7V9 
Go to UniProtKB:  Q9D7V9
IMPC:  MGI:1914361
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D7V9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download Ideal Coordinates CCD File 
U [auth D]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
N [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
L [auth B],
T [auth D]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
I [auth B]
J [auth B]
K [auth B]
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
O [auth D],
P [auth D],
Q [auth D],
R [auth D],
S [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
B, D
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.205α = 90
b = 202.205β = 90
c = 45.596γ = 120
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
  • Version 1.7: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.8: 2023-11-15
    Changes: Data collection