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- PDB-6ael: Crystal structure of ENPP1 in complex with 3'3'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 6ael
TitleCrystal structure of ENPP1 in complex with 3'3'-cGAMP
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d
KeywordsIMMUNOSUPPRESSANT / Enzyme / Phoshodiesterase / cGAMP / cGAS-STING / cyclic GMP-AMP
Function / homology
Function and homology information


microglial cell migration / Vitamin B2 (riboflavin) metabolism / articular cartilage development / response to platelet-derived growth factor / ligamentous ossification / response to vitamin B6 / cellular response to sodium phosphate / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / organic phosphonate metabolic process ...microglial cell migration / Vitamin B2 (riboflavin) metabolism / articular cartilage development / response to platelet-derived growth factor / ligamentous ossification / response to vitamin B6 / cellular response to sodium phosphate / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / organic phosphonate metabolic process / inorganic diphosphate transport / post-embryonic forelimb morphogenesis / tooth mineralization / GTP diphosphatase activity / hematopoietic stem cell migration to bone marrow / leukocyte activation involved in inflammatory response / UTP diphosphatase activity / phosphodiesterase I / dinucleotide phosphatase activity / coenzyme A diphosphatase activity / sensory perception of temperature stimulus / biomineral tissue development / bone growth / coenzyme A catabolic process / basal dendrite / nucleoside triphosphate catabolic process / vascular associated smooth muscle cell migration / nucleotide diphosphatase / inhibition of non-skeletal tissue mineralization / pyrophosphatase activity / response to Gram-positive bacterium / magnesium ion homeostasis / diphosphate metabolic process / endochondral bone morphogenesis / bone trabecula formation / vitamin D3 metabolic process / nucleoside triphosphate diphosphatase activity / cementum mineralization / vascular associated smooth muscle cell proliferation / central nervous system myelination / mucus secretion / bone mineralization involved in bone maturation / response to sodium phosphate / ATP diphosphatase activity / negative regulation of bone mineralization / sensory perception of mechanical stimulus / phosphate ion homeostasis / plasma cell differentiation / B-1 B cell homeostasis / phosphodiesterase I activity / scavenger receptor activity / artery development / collagen-activated signaling pathway / endochondral ossification / apoptotic process involved in development / microglia differentiation / apical dendrite / bone remodeling / phosphoric diester hydrolase activity / regulation of bone mineralization / cellular homeostasis / hormone metabolic process / inflammatory response to antigenic stimulus / negative regulation of ossification / oligodendrocyte apoptotic process / aorta development / cartilage development / middle ear morphogenesis / hydrolase activity, acting on ester bonds / odontogenesis / adult walking behavior / axon regeneration / fat pad development / polysaccharide binding / smoothened signaling pathway / skin development / muscle cell cellular homeostasis / response to ATP / spinal cord development / negative regulation of fat cell differentiation / bone mineralization / defense response to protozoan / fat cell differentiation / D-glucose import / phosphatase activity / response to dietary excess / macrophage differentiation / response to magnesium ion / T cell differentiation / 3',5'-cyclic-AMP phosphodiesterase activity / fibroblast growth factor receptor signaling pathway / vasculogenesis / adipose tissue development / bone resorption / calcium ion homeostasis / ATP metabolic process / ossification / osteoclast differentiation / adult locomotory behavior / kidney development
Similarity search - Function
Somatomedin B domain, chordata / 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 ...Somatomedin B domain, chordata / 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
Similarity search - Domain/homology
Chem-4BW / Ectonucleotide pyrophosphatase/phosphodiesterase 1 / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKato, K. / Nishimasu, H. / Hirano, S. / Hirano, H. / Ishitani, R. / Nureki, O.
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1.
Authors: Kato, K. / Nishimasu, H. / Oikawa, D. / Hirano, S. / Hirano, H. / Kasuya, G. / Ishitani, R. / Tokunaga, F. / Nureki, O.
History
DepositionAug 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: 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.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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 2.1Nov 22, 2023Group: 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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,62123
Polymers84,8161
Non-polymers2,80522
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint6 kcal/mol
Surface area28570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.169, 94.063, 74.274
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1


Mass: 84816.156 Da / Num. of mol.: 1 / Mutation: T238A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Enpp1, mCG_9001 / Production host: Homo sapiens (human) / References: UniProt: G3X9S2, UniProt: P06802*PLUS

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 3
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 , 6 types, 374 molecules

#4: Chemical ChemComp-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsProtease recognition site

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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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG3350, 0.1 M Bis-Tris propane, pH 8.5, 0.2 M NaBr and 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47 Å / Num. obs: 57243 / % possible obs: 100 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.751 / Num. unique obs: 57214

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GTW

4gtw


Resolution: 1.9→47 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.25
RfactorNum. reflection% reflection
Rfree0.202 2894 5.06 %
Rwork0.1662 --
obs0.168 57214 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5820 0 167 356 6343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076200
X-RAY DIFFRACTIONf_angle_d0.8718458
X-RAY DIFFRACTIONf_dihedral_angle_d13.9943682
X-RAY DIFFRACTIONf_chiral_restr0.053921
X-RAY DIFFRACTIONf_plane_restr0.0051073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93120.31831320.25782549X-RAY DIFFRACTION100
1.9312-1.96450.32891350.23992606X-RAY DIFFRACTION100
1.9645-2.00020.27321410.22362565X-RAY DIFFRACTION100
2.0002-2.03870.24491370.21072580X-RAY DIFFRACTION100
2.0387-2.08030.23121500.19912525X-RAY DIFFRACTION100
2.0803-2.12550.22271290.19812641X-RAY DIFFRACTION100
2.1255-2.1750.24141430.18752547X-RAY DIFFRACTION100
2.175-2.22930.20651100.17482594X-RAY DIFFRACTION100
2.2293-2.28960.23521340.18022577X-RAY DIFFRACTION100
2.2896-2.3570.22011440.17482582X-RAY DIFFRACTION100
2.357-2.43310.2111350.16932578X-RAY DIFFRACTION100
2.4331-2.520.19321350.16722599X-RAY DIFFRACTION100
2.52-2.62090.20011370.16582564X-RAY DIFFRACTION100
2.6209-2.74020.20651430.16562590X-RAY DIFFRACTION100
2.7402-2.88460.22231320.16862589X-RAY DIFFRACTION100
2.8846-3.06530.21091360.16542585X-RAY DIFFRACTION100
3.0653-3.3020.19851450.16022600X-RAY DIFFRACTION100
3.302-3.63410.17481380.15592601X-RAY DIFFRACTION100
3.6341-4.15970.1741520.14212593X-RAY DIFFRACTION100
4.1597-5.23970.16991430.13842601X-RAY DIFFRACTION100
5.2397-47.04590.18661430.16052654X-RAY DIFFRACTION100
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)
10.9660.17610.16532.7042-0.11271.708-0.06710.10660.0949-0.52030.1412-0.2521-0.1640.1033-0.05930.2604-0.05360.06540.1749-0.01980.143511.42824.3622-5.8461
21.5975-0.3578-0.22652.60630.54751.2569-0.1592-0.3262-0.07860.71670.2935-0.59680.29350.1952-0.07050.39360.1154-0.16750.2803-0.02650.272221.7994-6.772127.4805
30.7556-0.45020.06673.40170.24940.9045-0.0974-0.11870.09680.25830.147-0.2955-0.0544-0.0021-0.04430.15150.0153-0.01260.1764-0.02640.125113.15958.563416.2439
41.44260.11850.32482.1562-0.04171.4219-0.15130.4102-0.0832-0.77280.27390.0596-0.123-0.01550.0060.5208-0.11230.02750.2941-0.02220.12955.4083-6.9045-16.0927
51.07580.35490.03082.1194-0.73732.7393-0.29980.32770.2095-0.91050.32440.1086-0.21680.1633-0.04390.6942-0.144-0.03850.29740.02340.21424.38616.6633-20.5785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 734 through 903 )
2X-RAY DIFFRACTION2chain 'A' and (resid 170 through 415 )
3X-RAY DIFFRACTION3chain 'A' and (resid 416 through 576 )
4X-RAY DIFFRACTION4chain 'A' and (resid 577 through 664 )
5X-RAY DIFFRACTION5chain 'A' and (resid 665 through 733 )

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