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


This is version 1.5 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
  • Structures With Same Primary Citation

  • 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 hydrolas ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acylethanolamine-hydrolyzing acid amidase subunit alpha
A, C
107Mus musculusMutation(s): 0 
Gene Names: NaaaAsahl
EC: 3.5.1.60
Find proteins for Q9D7V9 (Mus musculus)
Go to UniProtKB:  Q9D7V9
NIH Common Fund Data Resources
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
N-acylethanolamine-hydrolyzing acid amidase subunit beta
B, D
232Mus musculusMutation(s): 0 
Gene Names: NaaaAsahl
EC: 3.5.1.60
Find proteins for Q9D7V9 (Mus musculus)
Go to UniProtKB:  Q9D7V9
NIH Common Fund Data Resources
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download CCD File 
D
3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PG4
Query on PG4

Download CCD File 
B, D
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
B,DL-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



Entry History & Funding Information

Deposition Data


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

Revision History 

  • 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