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- PDB-6dy1: Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) with fa... -

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Basic information

Entry
Database: PDB / ID: 6dy1
TitleRabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) with fatty acid (myristate), in presence of Triton X-100
Components(N-acylethanolamine acid amidase ...) x 2
KeywordsHYDROLASE / endocannabinoid / lipase
Function / homology
Function and homology information


N-(long-chain-acyl)ethanolamine deacylase / sphingosine metabolic process / N-(long-chain-acyl)ethanolamine deacylase activity / ceramidase / N-acylsphingosine amidohydrolase activity / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process / fatty acid metabolic process ...N-(long-chain-acyl)ethanolamine deacylase / sphingosine metabolic process / N-(long-chain-acyl)ethanolamine deacylase activity / ceramidase / N-acylsphingosine amidohydrolase activity / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process / fatty acid metabolic process / lysosome / membrane
Similarity search - Function
Acid ceramidase-like / Acid ceramidase, N-terminal / beta subunit of N-acylethanolamine-hydrolyzing acid amidase / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family
Similarity search - Domain/homology
MYRISTIC ACID / Chem-TON / N-acylethanolamine-hydrolyzing acid amidase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.998 Å
AuthorsGorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Molecular mechanism of activation of the immunoregulatory amidase NAAA.
Authors: Gorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B.
History
DepositionJul 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.3Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Apr 17, 2019Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_ec
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acylethanolamine acid amidase alpha-subunit
B: N-acylethanolamine acid amidase beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,76725
Polymers38,3812
Non-polymers2,38723
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-170 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.351, 159.351, 159.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

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N-acylethanolamine acid amidase ... , 2 types, 2 molecules AB

#1: Protein N-acylethanolamine acid amidase alpha-subunit


Mass: 12124.106 Da / Num. of mol.: 1 / Fragment: residues 3-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: G1T7U7, N-(long-chain-acyl)ethanolamine deacylase
#2: Protein N-acylethanolamine acid amidase beta-subunit


Mass: 26256.689 Da / Num. of mol.: 1 / Fragment: CBAH domain residues 99-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: G1T7U7, N-(long-chain-acyl)ethanolamine deacylase

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Sugars , 1 types, 3 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 109 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TON / 2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL


Mass: 294.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H30O3
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.1 M (NH4)2SO4 with 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.998→50 Å / Num. obs: 14498 / % possible obs: 100 % / Redundancy: 73.2 % / Net I/σ(I): 43
Reflection shellResolution: 2.998→3.11 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U7Z

5u7z


Resolution: 2.998→46.001 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.92
RfactorNum. reflection% reflection
Rfree0.2331 1780 10.01 %
Rwork0.194 --
obs0.198 17785 67.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.998→46.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 137 89 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042804
X-RAY DIFFRACTIONf_angle_d0.6543837
X-RAY DIFFRACTIONf_dihedral_angle_d9.5081625
X-RAY DIFFRACTIONf_chiral_restr0.043425
X-RAY DIFFRACTIONf_plane_restr0.003476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9981-3.07910.3684420.3258372X-RAY DIFFRACTION21
3.0791-3.16970.34411030.3077933X-RAY DIFFRACTION51
3.1697-3.2720.32281090.2782972X-RAY DIFFRACTION54
3.272-3.38890.33891080.2727982X-RAY DIFFRACTION54
3.3889-3.52460.30571090.2593974X-RAY DIFFRACTION54
3.5246-3.68490.28341080.2327976X-RAY DIFFRACTION54
3.6849-3.87910.24931100.205990X-RAY DIFFRACTION54
3.8791-4.1220.2171150.19581039X-RAY DIFFRACTION58
4.122-4.440.21821640.15661523X-RAY DIFFRACTION83
4.44-4.88640.14512020.12821812X-RAY DIFFRACTION100
4.8864-5.59240.18452030.14811801X-RAY DIFFRACTION100
5.5924-7.04170.2162040.19511827X-RAY DIFFRACTION100
7.0417-46.00610.2542030.20841804X-RAY DIFFRACTION99

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