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- PDB-5ege: Structure of ENPP6, a choline-specific glycerophosphodiester-phos... -

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Entry
Database: PDB / ID: 5ege
TitleStructure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 6
KeywordsHYDROLASE / Choline metabolism / Phosphodiesterase
Function / homology
Function and homology information


glycerophosphocholine cholinephosphodiesterase / glycerophosphocholine cholinephosphodiesterase activity / Glycerophospholipid catabolism / glycerophosphodiester phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / choline metabolic process / lipid catabolic process / lipid metabolic process / extracellular region ...glycerophosphocholine cholinephosphodiesterase / glycerophosphocholine cholinephosphodiesterase activity / Glycerophospholipid catabolism / glycerophosphodiester phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / choline metabolic process / lipid catabolic process / lipid metabolic process / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Gyrase A; domain 2 - #180 / 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 / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycerophosphocholine cholinephosphodiesterase ENPP6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMorita, J. / Kano, K. / Kato, K. / Takita, H. / Ishitani, R. / Nishimasu, H. / Nureki, O. / Aoki, J.
CitationJournal: Sci Rep / Year: 2016
Title: Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase
Authors: Morita, J. / Kano, K. / Kato, K. / Takita, H. / Sakagami, H. / Yamamoto, Y. / Mihara, E. / Ueda, H. / Sato, T. / Tokuyama, H. / Arai, H. / Asou, H. / Takagi, J. / Ishitani, R. / Nishimasu, H. ...Authors: Morita, J. / Kano, K. / Kato, K. / Takita, H. / Sakagami, H. / Yamamoto, Y. / Mihara, E. / Ueda, H. / Sato, T. / Tokuyama, H. / Arai, H. / Asou, H. / Takagi, J. / Ishitani, R. / Nishimasu, H. / Nureki, O. / Aoki, J.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_validate_close_contact / 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 / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 6
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
C: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
D: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,81933
Polymers198,3954
Non-polymers6,42429
Water36,8952048
1
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2919
Polymers49,5991
Non-polymers1,6928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-6 kcal/mol
Surface area16280 Å2
MethodPISA
2
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2298
Polymers49,5991
Non-polymers1,6307
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-8 kcal/mol
Surface area16280 Å2
MethodPISA
3
C: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2919
Polymers49,5991
Non-polymers1,6928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area16350 Å2
MethodPISA
4
D: Ectonucleotide pyrophosphatase/phosphodiesterase family member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0087
Polymers49,5991
Non-polymers1,4096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-14 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.290, 78.240, 103.640
Angle α, β, γ (deg.)90.040, 89.980, 114.610
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 / NPP-6 / Choline-specific glycerophosphodiester phosphodiesterase / Glycerophosphocholine ...NPP-6 / Choline-specific glycerophosphodiester phosphodiesterase / Glycerophosphocholine cholinephosphodiesterase / GPC-Cpde


Mass: 49598.664 Da / Num. of mol.: 4 / Fragment: UNP residues 1-421 / Mutation: C393A, C412S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Enpp6 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: Q8BGN3, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases, glycerophosphocholine cholinephosphodiesterase

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Sugars , 3 types, 15 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 4
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
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
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 , 3 types, 2062 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2048 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5 / Details: ammonium chloride, sodium acetate pH, PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.282 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 120105 / % possible obs: 97 % / Redundancy: 4 % / Net I/σ(I): 6.11
Reflection shellRejects: 0

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
Cootmodel building
PHENIX(1.10_2155: 000)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→41.896 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2057 5988 4.99 %
Rwork0.167 114096 -
obs0.1689 120084 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.01 Å2 / Biso mean: 22.2974 Å2 / Biso min: 7.19 Å2
Refinement stepCycle: final / Resolution: 2→41.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12804 0 394 2048 15246
Biso mean--38.53 31.05 -
Num. residues----1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713592
X-RAY DIFFRACTIONf_angle_d0.8918493
X-RAY DIFFRACTIONf_chiral_restr0.0592012
X-RAY DIFFRACTIONf_plane_restr0.0052319
X-RAY DIFFRACTIONf_dihedral_angle_d11.947985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.29942000.26113615381595
2.0227-2.04650.29171930.24483755394895
2.0465-2.07150.27771840.2323778396295
2.0715-2.09770.27942000.23413741394195
2.0977-2.12530.30291920.23323732392495
2.1253-2.15440.26581980.21363739393796
2.1544-2.18520.23891970.21093724392195
2.1852-2.21780.27771970.20233830402796
2.2178-2.25250.23732030.20053714391796
2.2525-2.28940.23811860.18813820400696
2.2894-2.32890.22811970.18843713391096
2.3289-2.37120.2372100.18213849405996
2.3712-2.41680.2511930.1783705389896
2.4168-2.46610.23432100.17413852406297
2.4661-2.51980.21722030.17383775397896
2.5198-2.57840.23662000.16593794399497
2.5784-2.64280.19022020.16633795399797
2.6428-2.71430.25461940.16323852404697
2.7143-2.79410.1932020.16373846404897
2.7941-2.88430.1972080.16273844405297
2.8843-2.98740.22981980.16423770396897
2.9874-3.10690.1961940.15233867406198
3.1069-3.24830.17811960.15083881407798
3.2483-3.41950.17222040.14883824402898
3.4195-3.63360.17162050.14973823402898
3.6336-3.91390.17342050.13893895410098
3.9139-4.30750.17322050.13533882408799
4.3075-4.92990.11862040.11623884408899
4.9299-6.2080.1732050.15433882408799
6.208-41.90560.21772030.17473915411899

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