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- PDB-6aek: Crystal structure of ENPP1 in complex with pApG -

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Basic information

Entry
Database: PDB / ID: 6aek
TitleCrystal structure of ENPP1 in complex with pApG
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 / cellular response to sodium phosphate / Vitamin B2 (riboflavin) metabolism / response to platelet-derived growth factor / articular cartilage development / ligamentous ossification / : / organic phosphonate metabolic process / inorganic diphosphate transport / post-embryonic forelimb morphogenesis ...microglial cell migration / cellular response to sodium phosphate / Vitamin B2 (riboflavin) metabolism / response to platelet-derived growth factor / articular cartilage development / ligamentous ossification / : / organic phosphonate metabolic process / inorganic diphosphate transport / post-embryonic forelimb morphogenesis / response to vitamin B6 / tooth mineralization / GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / hematopoietic stem cell migration to bone marrow / UTP diphosphatase activity / dinucleotide phosphatase activity / coenzyme A diphosphatase activity / basal dendrite / coenzyme A catabolic process / vascular associated smooth muscle cell migration / biomineral tissue development / phosphodiesterase I / nucleotide diphosphatase / sensory perception of temperature stimulus / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / nucleoside triphosphate catabolic process / bone growth / pyrophosphatase activity / endochondral bone morphogenesis / bone trabecula formation / diphosphate metabolic process / inhibition of non-skeletal tissue mineralization / response to Gram-positive bacterium / vascular associated smooth muscle cell proliferation / mucus secretion / vitamin D3 metabolic process / magnesium ion homeostasis / cementum mineralization / nucleoside triphosphate diphosphatase activity / bone mineralization involved in bone maturation / response to sodium phosphate / ATP diphosphatase activity / negative regulation of glycogen biosynthetic process / sensory perception of mechanical stimulus / B-1 B cell homeostasis / negative regulation of bone mineralization / central nervous system myelination / phosphate ion homeostasis / artery development / negative regulation of D-glucose import across plasma membrane / collagen-activated signaling pathway / endochondral ossification / melanocyte differentiation / microglia differentiation / regulation of bone mineralization / phosphoric diester hydrolase activity / bone remodeling / inflammatory response to antigenic stimulus / intracellular phosphate ion homeostasis / phosphate-containing compound metabolic process / apical dendrite / plasma cell differentiation / hormone metabolic process / oligodendrocyte apoptotic process / cartilage development / negative regulation of ossification / phosphodiesterase I activity / axon regeneration / odontogenesis / scavenger receptor activity / adult walking behavior / fat pad development / exonuclease activity / : / aorta development / smoothened signaling pathway / middle ear morphogenesis / skin development / protein poly-ADP-ribosylation / defense response to protozoan / negative regulation of fat cell differentiation / spinal cord development / bone mineralization / response to dietary excess / response to ATP / polysaccharide binding / phosphatase activity / macrophage differentiation / T cell differentiation / 3',5'-cyclic-AMP phosphodiesterase activity / fibroblast growth factor receptor signaling pathway / response to magnesium ion / adipose tissue development / bone resorption / vasculogenesis / fat cell differentiation / ATP metabolic process / calcium ion homeostasis / cell projection
Similarity search - Function
Extracellular Endonuclease; Chain A / 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 ...Extracellular Endonuclease; Chain A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE MONOPHOSPHATE / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: 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_unobs_or_zero_occ_atoms / 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.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 / _pdbx_unobs_or_zero_occ_atoms.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 3.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id
Revision 3.1Oct 30, 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)87,53322
Polymers84,8161
Non-polymers2,71721
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint6 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.486, 94.071, 74.680
Angle α, β, γ (deg.)90.00, 96.86, 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 , 7 types, 339 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 17% PEG3350, 0.1 M Bis-Tris propane, pH 7.5, 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 6M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47 Å / Num. obs: 69252 / % possible obs: 100 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.662 / Num. unique obs: 69203

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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: 1.8→47 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.83
RfactorNum. reflection% reflection
Rfree0.208 3432 4.96 %
Rwork0.1831 --
obs0.1843 69203 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5806 0 160 322 6288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066156
X-RAY DIFFRACTIONf_angle_d0.8518402
X-RAY DIFFRACTIONf_dihedral_angle_d13.4743659
X-RAY DIFFRACTIONf_chiral_restr0.053920
X-RAY DIFFRACTIONf_plane_restr0.0061068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82470.39541360.37872654X-RAY DIFFRACTION100
1.8247-1.85070.3461460.33752586X-RAY DIFFRACTION100
1.8507-1.87840.37391310.31752686X-RAY DIFFRACTION100
1.8784-1.90770.31811370.28482573X-RAY DIFFRACTION100
1.9077-1.9390.26351310.26572636X-RAY DIFFRACTION100
1.939-1.97240.29361560.25712594X-RAY DIFFRACTION100
1.9724-2.00830.26371360.23452609X-RAY DIFFRACTION100
2.0083-2.04690.2381340.22182598X-RAY DIFFRACTION100
2.0469-2.08870.26931350.21522669X-RAY DIFFRACTION100
2.0887-2.13410.24081510.21122589X-RAY DIFFRACTION100
2.1341-2.18380.24991470.20512624X-RAY DIFFRACTION100
2.1838-2.23840.22051300.19442585X-RAY DIFFRACTION100
2.2384-2.29890.21551330.19552649X-RAY DIFFRACTION100
2.2989-2.36650.25491290.19392640X-RAY DIFFRACTION100
2.3665-2.44290.2251320.18582615X-RAY DIFFRACTION100
2.4429-2.53020.26211200.19982650X-RAY DIFFRACTION100
2.5302-2.63150.22921480.19262625X-RAY DIFFRACTION100
2.6315-2.75130.24251330.19192626X-RAY DIFFRACTION100
2.7513-2.89630.20781380.19452647X-RAY DIFFRACTION100
2.8963-3.07770.22971350.19282618X-RAY DIFFRACTION100
3.0777-3.31530.20311260.18392646X-RAY DIFFRACTION100
3.3153-3.64880.19111580.17052647X-RAY DIFFRACTION100
3.6488-4.17650.16411480.14432636X-RAY DIFFRACTION100
4.1765-5.26090.1481320.13352647X-RAY DIFFRACTION100
5.2609-47.05150.1531300.1512722X-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)
10.9475-0.11940.29632.37190.19361.2782-0.0744-0.2085-0.05090.39430.1931-0.3930.07770.0005-0.08630.2250.0598-0.03670.2777-0.02450.248418.1524-0.748823.2666
21.7422-0.62380.8692.3303-0.90222.9999-0.00590.3435-0.0202-0.71670.19430.04370.1173-0.2617-0.16930.4995-0.12040.01090.3438-0.02640.2574.9156-6.4612-16.4815
32.5483-0.71060.86732.5608-0.95223.2079-0.08040.40380.362-0.87340.1265-0.0748-0.47420.08780.01680.7213-0.15760.00460.39560.02250.28795.5437.3937-20.9227
41.2255-0.1081-0.00242.5952-0.14412.6998-0.07940.09370.0974-0.54520.1588-0.2384-0.26180.0306-0.06060.2985-0.07420.06820.2185-0.01870.205811.92074.1477-5.7234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 170 through 576 )
2X-RAY DIFFRACTION2chain 'A' and (resid 577 through 668 )
3X-RAY DIFFRACTION3chain 'A' and (resid 669 through 733 )
4X-RAY DIFFRACTION4chain 'A' and (resid 734 through 903 )

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