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Basic information

Entry
Database: PDB / ID: 8p90
TitleTARGET COMPLEX 2
ComponentsN-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
KeywordsMEMBRANE PROTEIN / Complex / Membrane / Enzyme / Transport / Vitamin B6
Function / homology
Function and homology information


N-acetylphosphatidylethanolamine-hydrolysing phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / Biosynthesis of A2E, implicated in retinal degradation / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / smooth endoplasmic reticulum membrane / host-mediated regulation of intestinal microbiota composition / phospholipid catabolic process / bile acid binding / photoreceptor outer segment membrane ...N-acetylphosphatidylethanolamine-hydrolysing phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / Biosynthesis of A2E, implicated in retinal degradation / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / smooth endoplasmic reticulum membrane / host-mediated regulation of intestinal microbiota composition / phospholipid catabolic process / bile acid binding / photoreceptor outer segment membrane / temperature homeostasis / positive regulation of brown fat cell differentiation / hippocampal mossy fiber to CA3 synapse / positive regulation of inflammatory response / nuclear envelope / presynaptic membrane / early endosome membrane / postsynaptic membrane / early endosome / neuron projection / Golgi membrane / neuronal cell body / Golgi apparatus / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
N-acyl-phosphatidylethanolamine-hydrolysing phospholipase D / Beta-lactamase superfamily domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / PYRIDOXAL-5'-PHOSPHATE / N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGarau, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Chem Biol / Year: 2025
Title: NAPE-PLD is target of thiazide diuretics.
Authors: Chiarugi, S. / Margheriti, F. / De Lorenzi, V. / Martino, E. / Margheritis, E.G. / Moscardini, A. / Marotta, R. / Chaves-Sanjuan, A. / Del Seppia, C. / Federighi, G. / Lapi, D. / Bandiera, T. ...Authors: Chiarugi, S. / Margheriti, F. / De Lorenzi, V. / Martino, E. / Margheritis, E.G. / Moscardini, A. / Marotta, R. / Chaves-Sanjuan, A. / Del Seppia, C. / Federighi, G. / Lapi, D. / Bandiera, T. / Rapposelli, S. / Scuri, R. / Bolognesi, M. / Garau, G.
History
DepositionJun 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_contact_author.email / _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
B: N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,23919
Polymers91,3092
Non-polymers5,93117
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.657, 94.657, 441.848
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11B-602-

DXC

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 57 through 71 or resid 73...
d_2ens_1(chain "B" and (resid 57 through 71 or resid 73...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERTHRTHRAA57 - 7157 - 71
d_12LYSLYSPROPROAA73 - 11573 - 115
d_13GLUGLUARGARGAA117 - 166117 - 166
d_14SERSERARGARGAA168 - 314168 - 314
d_15PHEPHELEULEUAA316 - 370316 - 370
d_16ALAALAASNASNAA372 - 388372 - 388
d_17ZNZNZNZNAC401
d_18ZNZNZNZNAD402
d_193PE3PE3PE3PEAE403
d_110DXCDXCDXCDXCAF404
d_111DXCDXCDXCDXCAG405
d_112DXCDXCDXCDXCAH406
d_113DXCDXCDXCDXCAI407
d_114DXCDXCDXCDXCAJ408
d_21SERSERTHRTHRBB57 - 7157 - 71
d_22LYSLYSPROPROBB73 - 11573 - 115
d_23GLUGLUARGARGBB117 - 166117 - 166
d_24SERSERARGARGBB168 - 314168 - 314
d_25PHEPHELEULEUBB316 - 370316 - 370
d_26ALAALAASNASNBB372 - 388372 - 388
d_27ZNZNZNZNBN603
d_28ZNZNZNZNBO604
d_293PE3PE3PE3PEBP605
d_210DXCDXCDXCDXCBL601
d_211DXCDXCDXCDXCBM602
d_212DXCDXCDXCDXCBQ606
d_213DXCDXCDXCDXCBR607
d_214DXCDXCDXCDXCBS608

NCS oper: (Code: givenMatrix: (-0.463218962981, -0.875942202915, -0.134734737492), (-0.875471334634, 0.428637455737, 0.223203659855), (-0.137761150434, 0.221348568305, -0.96541528719)Vector: 43. ...NCS oper: (Code: given
Matrix: (-0.463218962981, -0.875942202915, -0.134734737492), (-0.875471334634, 0.428637455737, 0.223203659855), (-0.137761150434, 0.221348568305, -0.96541528719)
Vector: 43.1182865734, -29.5779889157, 362.197308382)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D / N-acyl phosphatidylethanolamine phospholipase D / NAPE-PLD / NAPE-hydrolyzing phospholipase D


Mass: 45654.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAPEPLD, C7orf18 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6IQ20, N-acetylphosphatidylethanolamine-hydrolysing phospholipase D

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Non-polymers , 5 types, 47 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Chemical
ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 1 M LITHIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→46.28 Å / Num. obs: 32276 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 100.04 Å2 / Rmerge(I) obs: 0.36 / Net I/σ(I): 4.7
Reflection shellResolution: 2.74→3.48 Å / Num. unique obs: 3913 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→46.28 Å / SU ML: 0.5123 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2954 1506 5.01 %
Rwork0.2705 28538 -
obs0.2718 30044 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.96 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5457 0 388 30 5875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01076108
X-RAY DIFFRACTIONf_angle_d1.45038373
X-RAY DIFFRACTIONf_chiral_restr0.083891
X-RAY DIFFRACTIONf_plane_restr0.00911019
X-RAY DIFFRACTIONf_dihedral_angle_d21.69182192
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.83514631592 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.890.38211280.40542420X-RAY DIFFRACTION95.79
2.89-2.990.3961380.38752528X-RAY DIFFRACTION99.85
2.99-3.110.44571270.40712536X-RAY DIFFRACTION99.92
3.11-3.260.43931310.35762572X-RAY DIFFRACTION99.96
3.26-3.430.37461330.31932545X-RAY DIFFRACTION99.89
3.43-3.640.33421160.2952609X-RAY DIFFRACTION99.78
3.64-3.920.34061350.30692559X-RAY DIFFRACTION99.59
3.92-4.320.28041360.25412611X-RAY DIFFRACTION99.96
4.32-4.940.26481630.22562585X-RAY DIFFRACTION99.96
4.94-6.220.28041400.24672682X-RAY DIFFRACTION100
6.22-46.280.25081590.24842891X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: -3.11324185737 Å / Origin y: 25.3873418945 Å / Origin z: 187.21466447 Å
111213212223313233
T1.15010867345 Å20.278994404253 Å20.0411041915194 Å2-0.530379949182 Å2-0.00967875752841 Å2--0.778535675233 Å2
L1.59521243939 °2-0.0975834085621 °20.886593016553 °2-0.977860085873 °2-0.0211533766243 °2--2.29982773247 °2
S0.0140361959582 Å °0.149788440556 Å °-0.107152670878 Å °0.0603925598621 Å °-0.0554028871766 Å °0.130462483727 Å °-0.311892740178 Å °0.164453750847 Å °0.0149544372757 Å °
Refinement TLS groupSelection details: all

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