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- PDB-6f30: Crystal structure of ectonucleotide phosphodiesterase/pyrophospha... -

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Entry
Database: PDB / ID: 6f30
TitleCrystal structure of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) in complex with UDPGlcNAc
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 3
KeywordsHYDROLASE / enzyme / ectonucleotide phosphodiesterase/pyrophosphatase / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


GTP diphosphatase activity / bis(5'-adenosyl)-triphosphatase activity / negative regulation of mast cell activation involved in immune response / basophil activation involved in immune response / UTP diphosphatase activity / dinucleotide phosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / nucleoside triphosphate catabolic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / phosphodiesterase I ...GTP diphosphatase activity / bis(5'-adenosyl)-triphosphatase activity / negative regulation of mast cell activation involved in immune response / basophil activation involved in immune response / UTP diphosphatase activity / dinucleotide phosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / nucleoside triphosphate catabolic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / phosphodiesterase I / nucleotide diphosphatase / negative regulation of mast cell proliferation / regulation of smooth muscle cell differentiation / nucleoside triphosphate diphosphatase activity / pyrimidine nucleotide metabolic process / ATP diphosphatase activity / phosphate ion homeostasis / phosphate-containing compound metabolic process / phosphodiesterase I activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ATP metabolic process / negative regulation of inflammatory response / nucleic acid binding / apical plasma membrane / external side of plasma membrane / calcium ion binding / perinuclear region of cytoplasm / cell surface / extracellular region / zinc ion binding / ATP binding / plasma membrane
Similarity search - Function
Gyrase A; domain 2 - #180 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase ...Gyrase A; domain 2 - #180 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDohler, C. / Zebisch, M. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation477/13-2 Germany
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure and substrate binding mode of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3).
Authors: Dohler, C. / Zebisch, M. / Strater, N.
History
DepositionNov 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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
Revision 2.1Jan 17, 2024Group: 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 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,11221
Polymers170,7412
Non-polymers5,37119
Water10,989610
1
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06710
Polymers85,3701
Non-polymers2,6979
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,04411
Polymers85,3701
Non-polymers2,67410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.270, 127.682, 113.414
Angle α, β, γ (deg.)90.00, 97.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 / E-NPP 3 / B10 / Phosphodiesterase I beta / PD-Ibeta / Phosphodiesterase I/nucleotide ...E-NPP 3 / B10 / Phosphodiesterase I beta / PD-Ibeta / Phosphodiesterase I/nucleotide pyrophosphatase 3 / RB13-6 antigen


Mass: 85370.336 Da / Num. of mol.: 2 / Mutation: T206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp3, Pdnp3 / Plasmid: pHLsec / Cell line (production host): HEK293S GntI- / Production host: Homo sapiens (human)
References: UniProt: P97675, phosphodiesterase I, nucleotide diphosphatase

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Sugars , 3 types, 11 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.: 5
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
#7: 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.: 5
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, 618 molecules

#4: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 61.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M KCl, 0.1 M MgAcetate, 0.05 NaCacodylate pH 6.0, 10.2% (w/v) PEG8000, 1 mM CaCl2, 0.1 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2014
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.3→37.51 Å / Num. obs: 94004 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 56.7 Å2 / Rpim(I) all: 0.087 / Net I/σ(I): 9.9
Reflection shellResolution: 2.3→2.34 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimless1.6.18data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XR9

2xr9


Resolution: 2.3→37.51 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.935 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1916 2.04 %RANDOM
Rwork0.196 ---
obs0.197 94000 99.6 %-
Displacement parametersBiso mean: 60.69 Å2
Baniso -1Baniso -2Baniso -3
1-4.0904 Å20 Å27.8957 Å2
2---6.3499 Å20 Å2
3---2.2595 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.3→37.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11611 0 333 610 12554
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00712320HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9516820HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4201SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes303HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1768HARMONIC5
X-RAY DIFFRACTIONt_it12320HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion17.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1609SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14107SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 146 2.1 %
Rwork0.237 6819 -
all0.238 6965 -
obs--99.84 %
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)
11.65030.2478-0.35641.1196-0.2621.20530.15660.06140.0859-0.0192-0.04940.0543-0.2061-0.0745-0.1072-0.0309-0.0004-0.0592-0.12660.01-0.1619-12.108710.677633.3905
21.82240.3753-0.25491.5112-0.35041.28020.07340.1359-0.5085-0.0139-0.01120.21060.2165-0.3737-0.0622-0.1736-0.1241-0.1305-0.06770.03340.0382-37.1904-15.941640.9531
31.34090.39421.00591.39550.95842.36560.14060.0891-0.13220.40020.2136-0.25010.30910.5597-0.3542-0.14540.0792-0.0904-0.0433-0.0742-0.204814.0475-13.41620.8693
41.20880.71250.82572.15150.69422.7849-0.00930.11570.0468-0.09030.07770.3974-0.0276-0.0686-0.0683-0.17310.0127-0.0216-0.10810.0158-0.0514-11.6776-16.6417-26.1364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|140 - A|550}
2X-RAY DIFFRACTION2{A|551 - A|871 }
3X-RAY DIFFRACTION3{B|140 - B|550}
4X-RAY DIFFRACTION4{B|551 - B|871 }

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