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- PDB-6dxy: Murine N-acylethanolamine-hydrolyzing acid amidase (NAAA) -

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Basic information

Entry
Database: PDB / ID: 6dxy
TitleMurine N-acylethanolamine-hydrolyzing acid amidase (NAAA)
Components(N-acylethanolamine-hydrolyzing acid amidase subunit ...) x 2
KeywordsHYDROLASE / endocannabinoid / lipase
Function / homology
Function and homology information


Neurotransmitter release cycle / : / 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 ...Neurotransmitter release cycle / : / 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 / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / lipid catabolic process / fatty acid metabolic process / DNA-binding transcription factor binding / lysosome / membrane / cytoplasm
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
N-acylethanolamine-hydrolyzing acid amidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 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 / struct / Item: _entity.pdbx_ec / _struct.pdbx_descriptor
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.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _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 1.8Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,17321
Polymers76,4054
Non-polymers1,76817
Water8,251458
1
A: N-acylethanolamine-hydrolyzing acid amidase subunit alpha
B: N-acylethanolamine-hydrolyzing acid amidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,01610
Polymers38,2022
Non-polymers8148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-83 kcal/mol
Surface area13880 Å2
MethodPISA
2
C: N-acylethanolamine-hydrolyzing acid amidase subunit alpha
D: N-acylethanolamine-hydrolyzing acid amidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,15711
Polymers38,2022
Non-polymers9559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-94 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.205, 202.205, 45.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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N-acylethanolamine-hydrolyzing acid amidase subunit ... , 2 types, 4 molecules ACBD

#1: Protein N-acylethanolamine-hydrolyzing acid amidase subunit alpha / N-acylsphingosine amidohydrolase-like / ASAH-like protein


Mass: 12077.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Naaa, Asahl / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9D7V9, N-(long-chain-acyl)ethanolamine deacylase
#2: Protein N-acylethanolamine-hydrolyzing acid amidase subunit beta / N-acylsphingosine amidohydrolase-like / ASAH-like protein


Mass: 26124.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Naaa, Asahl / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9D7V9, 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 , 4 types, 472 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M NaCl, 0.1 M BIS-TRIS pH 5 and 20 % PEG 3350

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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: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.851→50 Å / Num. obs: 58028 / % possible obs: 98 % / Redundancy: 8.1 % / Net I/σ(I): 16.5
Reflection shellResolution: 1.851→1.92 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: 1.851→40.441 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.91
RfactorNum. reflection% reflection
Rfree0.1916 2831 3.89 %
Rwork0.1674 --
obs0.1684 72758 61.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.851→40.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 101 458 5707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045438
X-RAY DIFFRACTIONf_angle_d0.757424
X-RAY DIFFRACTIONf_dihedral_angle_d10.3153203
X-RAY DIFFRACTIONf_chiral_restr0.047826
X-RAY DIFFRACTIONf_plane_restr0.004938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8514-1.88330.339170.3097480X-RAY DIFFRACTION8
1.8833-1.91750.3535350.2711761X-RAY DIFFRACTION13
1.9175-1.95440.2933450.26391132X-RAY DIFFRACTION20
1.9544-1.99430.2921720.26261806X-RAY DIFFRACTION31
1.9943-2.03770.23971090.23832548X-RAY DIFFRACTION45
2.0377-2.08510.2931160.23632847X-RAY DIFFRACTION49
2.0851-2.13720.23161120.21332805X-RAY DIFFRACTION50
2.1372-2.1950.20511170.19522852X-RAY DIFFRACTION50
2.195-2.25960.20721150.19572832X-RAY DIFFRACTION50
2.2596-2.33250.19861200.18632939X-RAY DIFFRACTION52
2.3325-2.41580.18791250.17123137X-RAY DIFFRACTION55
2.4158-2.51260.19361350.17823424X-RAY DIFFRACTION60
2.5126-2.62690.17291640.17063945X-RAY DIFFRACTION70
2.6269-2.76540.22851980.17084941X-RAY DIFFRACTION87
2.7654-2.93860.19112270.1655543X-RAY DIFFRACTION97
2.9386-3.16540.18922310.15875616X-RAY DIFFRACTION99
3.1654-3.48380.1942290.15225573X-RAY DIFFRACTION98
3.4838-3.98750.18592250.14435567X-RAY DIFFRACTION98
3.9875-5.02230.16222240.13655521X-RAY DIFFRACTION97
5.0223-40.45060.17232150.18265658X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4735-0.10180.5624.9087-1.18981.5537-0.01220.38990.33560.0196-0.0838-0.2701-0.1708-0.1012-0.02930.27460.0427-0.0180.20070.04050.1475-45.3809160.9561-22.4467
24.86650.3804-1.76876.23720.30322.79340.0976-0.2096-0.8305-0.1876-0.13450.46890.6753-0.70370.04070.2935-0.0958-0.08650.43620.02240.3385-54.2497148.3567-21.5172
31.4391.7797-0.40894.2192-1.20142.9910.4845-0.19850.36130.1925-0.20421.2175-0.2864-2.0098-0.19870.7907-0.26150.21781.866-0.08110.7533-67.4445153.8569-7.4348
45.49671.1170.41264.8660.49424.04510.0852-0.3070.21990.46840.07460.0904-0.0927-0.7752-0.06690.20570.03240.00010.52080.01430.2329-59.2199156.5974-15.5018
52.1555-0.93311.48021.70890.323.87580.0616-0.1667-0.068-0.0149-0.03430.1613-0.005-0.5312-0.03920.1418-0.0035-0.00550.16450.01380.1552-43.6869155.0029-7.9073
62.0568-0.47840.12832.67630.37973.4777-0.0101-0.19730.04840.16680.0559-0.1004-0.0955-0.11050.01270.1188-0.0126-0.03840.0982-0.01940.1285-37.8731154.2056-0.317
71.48880.11862.51322.04611.81917.0088-0.0113-0.56060.35220.5914-0.43430.85690.088-0.64450.25720.3221-0.01020.07120.3534-0.07610.2772-95.6706153.918325.4062
85.6925-1.9010.16014.606-0.76752.5703-0.1073-0.2304-0.22260.12330.0476-0.4205-0.08910.3570.1020.302-0.0704-0.02760.3743-0.01970.2387-80.6833153.471525.4556
95.0755-1.1356-0.39718.15592.99423.28760.2780.69190.46730.4018-0.0379-2.0246-0.09241.6322-0.24730.5685-0.1013-0.00541.2359-0.06870.6825-67.3914153.610310.3929
104.7141-1.99130.09133.7005-0.83115.46110.08260.2927-0.1384-0.1901-0.1922-0.0438-0.15550.38210.11690.2016-0.0658-0.04440.4323-0.020.3141-74.6938155.220418.8613
112.65650.50931.62662.9046-0.03743.83270.1466-0.2195-0.24870.10080.0063-0.08690.03650.0443-0.05350.1276-0.01970.02630.1682-0.01580.1757-95.9193152.115812.1418
122.4720.20871.79233.2662-0.44933.31720.03040.10520.1824-0.0925-0.0006-0.5151-0.14120.7704-0.22590.1919-0.0678-0.00340.3224-0.03070.2127-84.945157.94539.3709
132.42190.4495-0.28712.8690.2952.574-0.05750.22780.0842-0.38010.03080.0263-0.15140.00180.00280.1986-0.0182-0.02430.1782-0.00550.1355-94.744154.7891-2.4478
141.75951.15220.25183.10580.16823.2650.0434-0.19910.05470.14650.01930.3459-0.0055-0.2595-0.03860.1175-0.03030.02020.18640.00240.2137-102.4917148.6111.2946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 128 )
5X-RAY DIFFRACTION5chain 'B' and (resid 132 through 216 )
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 360 )
7X-RAY DIFFRACTION7chain 'C' and (resid 34 through 43 )
8X-RAY DIFFRACTION8chain 'C' and (resid 44 through 76 )
9X-RAY DIFFRACTION9chain 'C' and (resid 77 through 97 )
10X-RAY DIFFRACTION10chain 'C' and (resid 98 through 128 )
11X-RAY DIFFRACTION11chain 'D' and (resid 132 through 168 )
12X-RAY DIFFRACTION12chain 'D' and (resid 169 through 231 )
13X-RAY DIFFRACTION13chain 'D' and (resid 232 through 316 )
14X-RAY DIFFRACTION14chain 'D' and (resid 317 through 360 )

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