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- PDB-4qn9: Structure of human NAPE-PLD -

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Basic information

Entry
Database: PDB / ID: 4qn9
TitleStructure of human NAPE-PLD
ComponentsN-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
KeywordsHYDROLASE / PLD / NAPE / anandamide / bile acid / phospholipase / inflammation / pain / complex / NAE / AEA / OEA / PEA / MBL / PE / cannabinoid / fat / acyl / deoxycholate / obesity / phospholipid / membrane / steroid / drug / alpha-beta-beta-alpha fold / phosphodiesterase
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 modulation 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 modulation 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 / N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.652 Å
AuthorsGarau, G.
CitationJournal: Structure / Year: 2015
Title: Structure of human N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: regulation of fatty acid ethanolamide biosynthesis by bile acids.
Authors: Magotti, P. / Bauer, I. / Igarashi, M. / Babagoli, M. / Marotta, R. / Piomelli, D. / Garau, G.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)97,67322
Polymers91,3092
Non-polymers6,36420
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-202 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.099, 95.099, 444.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-603-

DXC

21B-712-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A - B1 - 900
2111B1 - 900

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.487812, -0.863244, -0.129806), (-0.858757, 0.447841, 0.248948), (-0.156771, 0.232912, -0.959779)44.03127, -34.25599, 362.82883

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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: C7orf18, NAPEPLD / Production host: Escherichia coli (E. coli)
References: UniProt: Q6IQ20, N-acetylphosphatidylethanolamine-hydrolysing phospholipase D

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Non-polymers , 5 types, 118 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#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 / 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.: 11 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.9 M lithium sulfate, 0.1 M HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.652→82.358 Å / Num. all: 35852 / Num. obs: 35841 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.1 % / Biso Wilson estimate: 72.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.7
Reflection shellResolution: 2.652→2.72 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CCP4refinement
MOLREPphasing
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.652→82.358 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.917 / SU B: 19.409 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25332 1794 5 %RANDOM
Rwork0.21407 ---
all0.216 34047 --
obs0.216 34047 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.844 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.77 Å20 Å2
2--0.77 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.652→82.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5252 0 415 98 5765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195984
X-RAY DIFFRACTIONr_bond_other_d0.0080.025612
X-RAY DIFFRACTIONr_angle_refined_deg2.3872.0248208
X-RAY DIFFRACTIONr_angle_other_deg1.541313057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.2255655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45223.773273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.87215881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2261532
X-RAY DIFFRACTIONr_chiral_restr0.290.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216305
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021331
Refine LS restraints NCSNumber: 5559 / Type: TIGHT THERMAL / Rms dev position: 3.54 Å / Weight position: 0.5
LS refinement shellResolution: 2.652→2.721 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 130 -
Rwork0.334 2439 -
obs--99.73 %
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)
12.63960.10430.93713.29531.32754.3922-0.03550.09630.24590.10310.0068-0.2815-0.60740.72410.02870.4771-0.0588-0.07330.3043-0.00790.102311.466332.3273201.6698
22.6595-1.16280.69013.2743-0.23772.71650.15410.2991-0.4007-0.1266-0.02050.24320.0338-0.0022-0.13360.23250.1279-0.03970.1175-0.06550.0773-15.651320.2661175.3768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 388
2X-RAY DIFFRACTION1A501 - 504
3X-RAY DIFFRACTION1B601 - 603
4X-RAY DIFFRACTION2B57 - 389
5X-RAY DIFFRACTION2A505 - 507
6X-RAY DIFFRACTION2B604 - 610

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