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- PDB-5tcd: Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine -

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Basic information

Entry
Database: PDB / ID: 5tcd
TitleHuman alkaline sphingomyelinase (ENPP7) in complex with phosphocholine
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 7
KeywordsHYDROLASE / sphingomyelinase / sphingomyelin / phosphocholine / glycosylphosphatidylinositol
Function / homology
Function and homology information


positive regulation of intestinal cholesterol absorption / regulation of intestinal lipid absorption / sphingomyelin metabolic process / positive regulation of sphingomyelin catabolic process / lipid digestion / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / positive regulation of ceramide biosynthetic process / glycosphingolipid catabolic process / Glycosphingolipid catabolism ...positive regulation of intestinal cholesterol absorption / regulation of intestinal lipid absorption / sphingomyelin metabolic process / positive regulation of sphingomyelin catabolic process / lipid digestion / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / positive regulation of ceramide biosynthetic process / glycosphingolipid catabolic process / Glycosphingolipid catabolism / phosphoric diester hydrolase activity / negative regulation of DNA replication / microvillus / fatty acid homeostasis / negative regulation of cell population proliferation / Golgi apparatus / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / PHOSPHOCHOLINE / Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsGorelik, A. / Liu, F. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Crystal structure of the human alkaline sphingomyelinase provides insights into substrate recognition.
Authors: Gorelik, A. / Liu, F. / Illes, K. / Nagar, B.
History
DepositionSep 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,64047
Polymers48,3801
Non-polymers7,26146
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.223, 104.223, 113.893
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase family member 7 / NPP-7 / Alkaline sphingomyelin phosphodiesterase / Intestinal alkaline sphingomyelinase / Alk-SMase


Mass: 48379.531 Da / Num. of mol.: 1 / Fragment: UNP residues 22-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENPP7, UNQ3077/PRO9912 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6UWV6, sphingomyelin phosphodiesterase

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Sugars , 4 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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, 246 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: I
#9: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.69 Å3/Da / Density % sol: 66.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: sodium iodide, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 65605 / % possible obs: 93.6 % / Redundancy: 5.2 % / Net I/σ(I): 17.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→38.444 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 3186 8.12 %
Rwork0.1727 --
obs0.1755 39213 72.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→38.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 198 205 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033409
X-RAY DIFFRACTIONf_angle_d0.614649
X-RAY DIFFRACTIONf_dihedral_angle_d12.9611983
X-RAY DIFFRACTIONf_chiral_restr0.041519
X-RAY DIFFRACTIONf_plane_restr0.003590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.43580.3279440.2426415X-RAY DIFFRACTION20
2.4358-2.47390.2744470.2241502X-RAY DIFFRACTION24
2.4739-2.51440.2272470.2561560X-RAY DIFFRACTION26
2.5144-2.55780.258530.2182649X-RAY DIFFRACTION30
2.5578-2.60430.2311690.2226721X-RAY DIFFRACTION33
2.6043-2.65440.2778750.2373840X-RAY DIFFRACTION39
2.6544-2.70850.31071020.2271014X-RAY DIFFRACTION47
2.7085-2.76740.26741100.23411214X-RAY DIFFRACTION57
2.7674-2.83180.28361340.22921457X-RAY DIFFRACTION68
2.8318-2.90260.29721340.21731602X-RAY DIFFRACTION72
2.9026-2.9810.23171520.21861648X-RAY DIFFRACTION77
2.981-3.06870.23631500.21551796X-RAY DIFFRACTION83
3.0687-3.16770.24521760.19922029X-RAY DIFFRACTION92
3.1677-3.28090.24771830.19052150X-RAY DIFFRACTION99
3.2809-3.41210.2271860.18012138X-RAY DIFFRACTION100
3.4121-3.56730.221900.16712148X-RAY DIFFRACTION100
3.5673-3.75530.17921940.1442174X-RAY DIFFRACTION100
3.7553-3.99030.16051960.14582149X-RAY DIFFRACTION100
3.9903-4.2980.19521960.13442168X-RAY DIFFRACTION100
4.298-4.72990.14981840.12712176X-RAY DIFFRACTION100
4.7299-5.41270.15741920.13062152X-RAY DIFFRACTION100
5.4127-6.81320.17821870.17682152X-RAY DIFFRACTION100
6.8132-38.44920.23711850.1992173X-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)
12.88980.52830.27571.14651.73913.7870.18530.2044-0.0949-0.3289-0.14480.15850.40790.2035-0.05880.33360.003-0.02910.1893-0.01350.127741.849230.335744.21
21.75820.1771-0.29092.0293-0.28752.53240.18410.13330.2316-0.2019-0.0050.28480.1227-0.2547-0.15650.2071-0.013-0.00490.25270.02220.168237.351343.037739.7568
33.18080.3061.94632.56694.33338.26410.0075-0.2877-0.3217-0.0612-0.07750.42860.731-0.69310.02330.4635-0.1696-0.06860.29790.02450.256933.320726.046546.5864
41.9624-0.0393-0.83572.5923-0.17240.83590.1467-0.20680.09470.20820.02050.08740.2708-0.1584-0.17270.2391-0.00270.00120.3090.0090.146343.071238.799350.4829
51.89280.78041.67085.799-0.50093.1498-0.026-0.36160.87950.0083-0.069-0.205-0.87230.29360.06130.4233-0.10670.1080.4098-0.19120.584748.744464.226757.8166
61.5594-0.0261-0.24521.90130.26642.42330.1006-0.27290.3790.0510.1142-0.351-0.08180.6123-0.18530.2043-0.02010.04870.3676-0.07490.271752.432947.761451.1991
73.2750.45450.03482.105-1.1151.95720.14540.11170.0759-0.2527-0.03130.27920.332-0.0448-0.15780.46370.07090.05690.35490.0150.079850.78535.969428.0017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 209 )
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 232 )
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 264 )
5X-RAY DIFFRACTION5chain 'A' and (resid 265 through 292 )
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 383 )
7X-RAY DIFFRACTION7chain 'A' and (resid 384 through 417 )

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