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- PDB-4gtx: Crystal structure of mouse Enpp1 in complex with TMP -

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Basic information

Entry
Database: PDB / ID: 4gtx
TitleCrystal structure of mouse Enpp1 in complex with TMP
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
KeywordsHYDROLASE / Bone Mineralization / Phosphodiesterase
Function / homology
Function and homology information


dinucleotide phosphatase activity / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / hydrolase activity, acting on ester bonds / phosphatidylcholine catabolic process / phospholipase D activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / phosphatidylcholine lysophospholipase activity ...dinucleotide phosphatase activity / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / hydrolase activity, acting on ester bonds / phosphatidylcholine catabolic process / phospholipase D activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / phosphatidylcholine lysophospholipase activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of epithelial cell migration / phospholipid metabolic process / chemotaxis / nucleic acid binding / immune response / calcium ion binding / extracellular space / extracellular region / zinc ion binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, 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. ...Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, 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
THYMIDINE-5'-PHOSPHATE / Ectonucleotide pyrophosphatase/phosphodiesterase 1 / Autotaxin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsKato, K. / Nishimasu, H. / Ishitani, R. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.
Authors: Kato, K. / Nishimasu, H. / Okudaira, S. / Mihara, E. / Ishitani, R. / Takagi, J. / Aoki, J. / Nureki, O.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jun 20, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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 2.2Oct 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 family member 2, Alkaline phosphodiesterase I
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,48916
Polymers189,1202
Non-polymers3,36814
Water00
1
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5698
Polymers94,5601
Non-polymers2,0087
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9208
Polymers94,5601
Non-polymers1,3607
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.723, 105.723, 174.442
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I / E-NPP 2 / Autotaxin / Extracellular lysophospholipase D / LysoPLD / Ectonucleotide ...E-NPP 2 / Autotaxin / Extracellular lysophospholipase D / LysoPLD / Ectonucleotide pyrophosphatase/phosphodiesterase 1 / isoform CRA_d


Mass: 94560.203 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 51-59, 92-905 / Mutation: K59R
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF ENPP2 (UNP RESIDUES 51-59) AND ENPP1 (UNP RESIDUES 92-905)
Source: (gene. exp.) Mus musculus (house mouse) / Cell: mammalian cells / Gene: Enpp2, Npps2, Pdnp2, Enpp1, mCG_9001 / Plasmid: modified pcDNA3.1 / Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human)
References: UniProt: Q9R1E6, UniProt: G3X9S2, alkylglycerophosphoethanolamine phosphodiesterase

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Sugars , 3 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}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.: 1
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 / 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.: 4
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, 8 molecules

#5: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#6: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY
Sequence detailsTHE FUSION PROTEIN OF ENPP2 (UNP RESIDUES 51-59) AND ENPP1 (UNP RESIDUES 92-905)

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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: 2.98 Å3/Da / Density % sol: 58.67 % / Mosaicity: 0.875 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: PEG 600, MgOAc, NaCl, ZnSO4, pH 4.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 34884 / Num. obs: 34884 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.123 / Χ2: 1.751 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.262.40.3615950.711192
3.26-3.312.40.3517150.748192.6
3.31-3.382.60.33616760.815194.2
3.38-3.452.70.3316770.861194.3
3.45-3.522.80.31517500.959194.9
3.52-3.62.90.29516820.98195.6
3.6-3.693.10.26417431.082196.5
3.69-3.793.20.23717471.114197
3.79-3.913.40.24217391.273196.6
3.91-4.033.50.20217531.352198
4.03-4.183.80.18717841.556198
4.18-4.343.90.15817571.68198.2
4.34-4.544.10.14117411.975198.6
4.54-4.784.20.12618112.052198.9
4.78-5.084.30.11418052.122199.1
5.08-5.474.30.12217511.99198.9
5.47-6.024.30.12117742.172198.9
6.02-6.894.50.10417762.288198.9
6.89-8.6750.07418072.548199.7
8.67-505.40.04618012.598199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GTW

4gtw


Resolution: 3.201→49.085 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8146 / SU ML: 1.01 / σ(F): 2.14 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 1765 5.06 %
Rwork0.2179 --
all0.2202 34864 -
obs0.2202 34864 97.07 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.638 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 246.12 Å2 / Biso mean: 81.3991 Å2 / Biso min: 22.45 Å2
Baniso -1Baniso -2Baniso -3
1-8.8132 Å2-0 Å20 Å2
2--8.8132 Å20 Å2
3----17.6264 Å2
Refinement stepCycle: LAST / Resolution: 3.201→49.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11007 0 204 0 11211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711587
X-RAY DIFFRACTIONf_angle_d0.83315780
X-RAY DIFFRACTIONf_chiral_restr0.0451760
X-RAY DIFFRACTIONf_plane_restr0.0042006
X-RAY DIFFRACTIONf_dihedral_angle_d15.6444164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2007-3.28720.36631290.34672412254192
3.2872-3.38390.35861320.33462440257294
3.3839-3.49310.35541300.31322457258795
3.4931-3.61790.34191320.29112543267595
3.6179-3.76270.28731420.25632530267297
3.7627-3.93390.31141420.2252550269297
3.9339-4.14120.24161400.1942549268998
4.1412-4.40050.2391390.17042613275298
4.4005-4.740.21141350.15162564269999
4.74-5.21650.20341420.16462603274599
5.2165-5.97020.25351400.19252603274399
5.9702-7.51750.25131250.1962626275199
7.5175-49.09090.22981370.208626092746100
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)
10.6798-0.4534-0.10650.626-0.63721.32190.0475-0.4331-0.1910.37550.15940.19870.1929-0.32560.03810.4283-0.01440.05280.30320.09610.417521.084314.964929.9844
21.17490.0241-0.64980.0233-0.01030.36860.0547-0.47740.22340.0273-0.09930.0787-0.35280.0503-0.70150.93190.18890.03010.4416-0.25580.272832.589242.662244.0371
30.2818-0.20820.24550.4448-0.28830.24560.0525-0.3328-0.05590.37270.12880.0609-0.4033-0.19760.00790.53110.04070.06540.4484-0.11730.399326.698526.99827.8082
40.3925-0.24150.38560.2054-0.14760.4705-0.03760.19680.08080.15180.365-0.0161-0.1514-0.09160.18490.47320.04690.18560.1229-0.01830.451723.332752.21764.163
50.2403-0.36290.26240.6458-0.14420.93630.0190.11670.10260.27110.0876-0.1056-0.41080.1997-0.00480.60230.1080.15250.2398-0.14210.336132.596751.528915.5551
60.55090.01210.16480.9365-0.74491.42350.09070.4407-0.019-0.45040.12440.2974-0.1474-0.37940.06790.28350.1399-0.10410.6211-0.02270.49317.66536.7029-25.1995
70.33190.0963-0.22360.3231-0.14740.17320.14470.2901-0.0895-0.29550.0588-0.01240.62030.01180.15340.81090.253-0.01310.7502-0.28960.235735.386316.3552-37.271
80.6664-0.3044-0.17260.3634-0.38091.09870.00360.0969-0.0304-0.08690.1001-0.02890.67560.10750.0190.54650.1445-0.15680.1754-0.18490.409233.96377.4835-8.9119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 170:415)A170 - 415
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 416:481)A416 - 481
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 482:576)A482 - 576
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 577:664)A577 - 664
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 665:902)A665 - 902
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 170:415)B170 - 415
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 416:526)B416 - 526
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 527:902)B527 - 902

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