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- PDB-4gtw: Crystal structure of mouse Enpp1 in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 4gtw
TitleCrystal structure of mouse Enpp1 in complex with AMP
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 / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity ...dinucleotide phosphatase activity / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of oligodendrocyte differentiation / hydrolase activity, acting on ester bonds / negative regulation of cell-matrix adhesion / positive regulation of epithelial cell migration / positive regulation of focal adhesion assembly / estrous cycle / phospholipid metabolic process / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / cell chemotaxis / positive regulation of peptidyl-tyrosine phosphorylation / nucleic acid binding / immune response / calcium ion binding / positive regulation of cell population proliferation / extracellular space / zinc ion binding / extracellular region / membrane / metal ion binding / plasma membrane
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 superfamily / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / His-Me finger superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Ectonucleotide pyrophosphatase/phosphodiesterase 1 / Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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.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.ptnr2_label_seq_id / _struct_ref_seq_dif.details
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 2, Alkaline phosphodiesterase I
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,66416
Polymers190,2462
Non-polymers3,41814
Water2,180121
1
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1568
Polymers95,1231
Non-polymers2,0337
Water181
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)96,5088
Polymers95,1231
Non-polymers1,3857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.283, 105.283, 173.685
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: 95122.953 Da / Num. of mol.: 2 / 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) / 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-Acetylglucosamine


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 , 4 types, 129 molecules

#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#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
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.89 Å3/Da / Density % sol: 57.43 % / Mosaicity: 0.2 °
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: 0.979 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 58639 / Num. obs: 58977 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.206 / Χ2: 1.444 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.754.70.53328760.684197.5
2.75-2.85.20.52828910.596199.4
2.8-2.855.40.51829270.622199.5
2.85-2.915.40.51429660.621199.3
2.91-2.975.70.50228820.649199.6
2.97-3.045.80.49529320.657199.8
3.04-3.126.20.46229590.725199.6
3.12-3.26.50.43828810.752199.8
3.2-3.370.39729860.793199.9
3.3-3.47.40.36129300.858199.9
3.4-3.527.80.40729301.622199.9
3.52-3.668.10.35129071.728199.9
3.66-3.838.60.27929581.608199.9
3.83-4.038.90.26829882.0161100
4.03-4.299.40.15128931.29199.9
4.29-4.629.70.12229801.449199.9
4.62-5.08100.11129181.63199.9
5.08-5.819.80.12929701.779199.9
5.81-7.3210.10.10929141.872199.9
7.32-5010.90.0729513.436199.8

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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
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.875 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7884 / SU ML: 0.96 / σ(F): 2.03 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 2984 5.06 %
Rwork0.2308 --
all0.2331 --
obs0.2331 58639 99.72 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.762 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 192.47 Å2 / Biso mean: 48.2999 Å2 / Biso min: 1.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.485 Å2-0 Å2-0 Å2
2--1.485 Å2-0 Å2
3----2.9701 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11017 0 208 121 11346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411604
X-RAY DIFFRACTIONf_angle_d0.76315805
X-RAY DIFFRACTIONf_chiral_restr0.0431762
X-RAY DIFFRACTIONf_plane_restr0.0042008
X-RAY DIFFRACTIONf_dihedral_angle_d15.3294179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6995-2.74380.41691300.39252597272798
2.7438-2.79110.41251390.36222649278899
2.7911-2.84180.40581560.351726752831100
2.8418-2.89650.37481530.35022641279499
2.8965-2.95560.33561390.313426502789100
2.9556-3.01990.34071250.300826832808100
3.0199-3.09010.36881360.29827182854100
3.0901-3.16740.32141470.284326542801100
3.1674-3.2530.30471390.261526452784100
3.253-3.34870.32351430.241126442787100
3.3487-3.45670.27821510.234327172868100
3.4567-3.58020.3081470.224126452792100
3.5802-3.72350.23591450.210326622807100
3.7235-3.89290.25021410.187427122853100
3.8929-4.09810.20521210.174526612782100
4.0981-4.35470.21171430.171126882831100
4.3547-4.69070.21151440.158326692813100
4.6907-5.16220.2141480.163126662814100
5.1622-5.90810.23561640.190426602824100
5.9081-7.43940.2311280.199726962824100
7.4394-48.88260.25461450.216526612806100
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)
10.6823-0.1718-0.1130.641-0.24780.79470.0381-0.3186-0.13720.54520.14160.2084-0.197-0.24850.09580.49380.00370.0810.13440.03360.126723.375220.348832.3613
20.8514-0.010.18741.08630.38430.80360.0497-0.27730.04360.4170.12960.0067-0.1079-0.07880.15710.26670.04540.03670.0963-0.12630.143826.555226.374827.1436
30.38720.1501-0.14731.34060.00920.48440.2280.03080.16190.01480.06170.1722-0.2725-0.01550.11070.20670.07590.18160.03410.02120.30123.064251.58793.7921
40.7601-0.48270.25131.1494-0.1190.3290.0751-0.01850.28720.16250.0244-0.215-0.3532-0.0539-0.11140.4660.06120.18940.0926-0.08640.368833.881260.923412.7791
50.4906-0.1045-0.09750.8519-0.08620.77450.0549-0.14630.11930.31940.0977-0.1398-0.20310.1585-0.16860.04470.15940.1966-0.2537-0.28250.081531.575444.990216.6252
60.70210.13270.17130.8171-0.24920.66220.0580.6080.1028-0.58780.16910.18730.2298-0.37480.2355-0.36710.178-0.14660.3741-0.02740.066821.994329.9469-26.468
70.25960.0227-0.06190.5021-0.0240.1286-0.08780.0887-0.28390.0058-0.0414-0.02950.40260.079-0.2950.36880.071-0.0350.1633-0.15030.440733.8797-4.30780.1653
80.7931-0.2624-0.42740.8037-0.16250.8238-0.12360.1045-0.3638-0.05040.0024-0.13450.4390.14650.00210.37450.1652-0.09770.1458-0.12970.438539.3834-5.7589-5.5134
90.5469-0.1578-0.23040.614-0.07230.7267-0.01730.1809-0.177-0.0706-0.0549-0.14190.34560.2085-0.05270.00250.22560.0691-0.1101-0.40890.060137.22358.116-13.227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 170:481)A170 - 481
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 482:576)A482 - 576
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 577:664)A577 - 664
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 665:758)A665 - 758
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 759:902)A759 - 902
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 170:591)B170 - 591
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 592:649)B592 - 649
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 650:734)B650 - 734
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 735:902)B735 - 902

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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