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- PDB-5lpg: Structure of NUDT15 in complex with 6-thio-GMP -

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Basic information

Entry
Database: PDB / ID: 5lpg
TitleStructure of NUDT15 in complex with 6-thio-GMP
ComponentsProbable 8-oxo-dGTP diphosphatase NUDT15
KeywordsHYDROLASE / MTH2 / DNA repair enzyme / Cancer
Function / homology
Function and homology information


nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection ...nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / Azathioprine ADME / xenobiotic catabolic process / regulation of proteasomal protein catabolic process / response to reactive oxygen species / mitotic cell cycle / metal ion binding / cytosol
Similarity search - Function
Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-71V / Nucleotide triphosphate diphosphatase NUDT15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMasuyer, G. / Carter, M. / Rehling, D. / Stenmark, P. / Helleday, T. / Jemth, A.-S. / Valerie, N.C.K. / Homan, E. / Herr, P. / Bevc, L. ...Masuyer, G. / Carter, M. / Rehling, D. / Stenmark, P. / Helleday, T. / Jemth, A.-S. / Valerie, N.C.K. / Homan, E. / Herr, P. / Bevc, L. / Page, B.D.G. / Hagenkort, A.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Sweden
CitationJournal: Cancer Res. / Year: 2016
Title: NUDT15 Hydrolyzes 6-Thio-DeoxyGTP to Mediate the Anticancer Efficacy of 6-Thioguanine.
Authors: Valerie, N.C. / Hagenkort, A. / Page, B.D. / Masuyer, G. / Rehling, D. / Carter, M. / Bevc, L. / Herr, P. / Homan, E. / Sheppard, N.G. / Stenmark, P. / Jemth, A.S. / Helleday, T.
History
DepositionAug 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 8-oxo-dGTP diphosphatase NUDT15
B: Probable 8-oxo-dGTP diphosphatase NUDT15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7718
Polymers37,2702
Non-polymers5016
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-64 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.502, 49.050, 135.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable 8-oxo-dGTP diphosphatase NUDT15 / 8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / ...8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / Nucleoside diphosphate-linked moiety X motif 15 / Nudix motif 15


Mass: 18635.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT15, MTH2 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NV35, 8-oxo-dGTP diphosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-71V / [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-sulfanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate / 6-Thio-GMP


Mass: 379.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG3350, 0.1M Tris pH 8.5, and 0.24M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.7→49 Å / Num. obs: 34988 / % possible obs: 99.9 % / Redundancy: 11.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rsym value: 0.037 / Net I/σ(I): 12.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.492 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5BON

5bon


Resolution: 1.7→49 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.326 / SU ML: 0.126 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25063 1751 5 %RANDOM
Rwork0.21617 ---
obs0.21795 33174 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--1.28 Å20 Å2
3----1.44 Å2
Refinement stepCycle: 1 / Resolution: 1.7→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 29 156 2674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192612
X-RAY DIFFRACTIONr_bond_other_d0.0030.022376
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9483556
X-RAY DIFFRACTIONr_angle_other_deg0.9033.0035494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8065314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90624.567127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4891510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212974
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02615
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5612.7471256
X-RAY DIFFRACTIONr_mcbond_other2.5612.7471255
X-RAY DIFFRACTIONr_mcangle_it4.0024.1071570
X-RAY DIFFRACTIONr_mcangle_other4.0014.1081571
X-RAY DIFFRACTIONr_scbond_it3.0623.1721356
X-RAY DIFFRACTIONr_scbond_other3.0623.1721356
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9464.5971986
X-RAY DIFFRACTIONr_long_range_B_refined7.55923.6013091
X-RAY DIFFRACTIONr_long_range_B_other7.52523.2993013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å
RfactorNum. reflection% reflection
Rfree0.439 111 -
Rwork-2437 -
obs--99.88 %
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)
10.54420.54140.47520.62430.6180.7581-0.05290.0642-0.1067-0.13560.1226-0.0794-0.24840.101-0.06970.1186-0.020.01940.04690.0040.0521-9.3946-9.035318.8891
20.71810.61711.3820.77251.30892.78090.1777-0.2307-0.02660.013-0.1451-0.12910.1726-0.4915-0.03260.0885-0.01720.02360.1202-0.02060.0611-27.2104-28.726713.9091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 1101
2X-RAY DIFFRACTION2B9 - 1104

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