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- PDB-9mbh: 8-Oxo-dGTP hydrolysis in human MTH1(G2K mutant) crystal using Mn2... -

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Basic information

Entry
Database: PDB / ID: 9mbh
Title8-Oxo-dGTP hydrolysis in human MTH1(G2K mutant) crystal using Mn2+: the ES-3M complex
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / Oxidized purine nucleoside triphosphate hydrolase
Function / homology
Function and homology information


2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins ...2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.21 Å
AuthorsHirata, K. / Nakamura, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Neutron and time-resolved X-ray crystallography reveal the substrate recognition and catalytic mechanism of human Nudix hydrolase MTH1.
Authors: Hirata, K. / Fujimiya, K. / Ostermann, A. / Schrader, T.E. / Hiromoto, T. / Goto, M. / Arimori, T. / Hirano, Y. / Kusaka, K. / Tamada, T. / Nakamura, T.
History
DepositionMar 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-dihydro-8-oxoguanine triphosphatase
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,55514
Polymers36,0872
Non-polymers1,46812
Water7,260403
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7787
Polymers18,0441
Non-polymers7346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-4 kcal/mol
Surface area8330 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7787
Polymers18,0441
Non-polymers7346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.488, 47.612, 123.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 7,8-dihydro-8-oxoguanine triphosphatase / MutT homologue-1 / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked ...MutT homologue-1 / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 18043.590 Da / Num. of mol.: 2 / Fragment: UNP residues 42-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, cacodylate, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→25.96 Å / Num. obs: 84684 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.92 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 29.1
Reflection shellResolution: 1.21→1.23 Å / Rmerge(I) obs: 0.556 / Num. unique obs: 4141

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.21→25.96 Å / SU ML: 0.1021 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.0939 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1714 4224 4.99 %
Rwork0.1393 80381 -
obs0.141 84605 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.94 Å2
Refinement stepCycle: LAST / Resolution: 1.21→25.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 74 403 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782903
X-RAY DIFFRACTIONf_angle_d1.21853964
X-RAY DIFFRACTIONf_chiral_restr0.0768407
X-RAY DIFFRACTIONf_plane_restr0.0079514
X-RAY DIFFRACTIONf_dihedral_angle_d16.23951113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.24411530.20822558X-RAY DIFFRACTION97.06
1.22-1.240.24631250.19292624X-RAY DIFFRACTION99.42
1.24-1.250.20741240.17752690X-RAY DIFFRACTION99.4
1.25-1.270.20471230.16882619X-RAY DIFFRACTION99.6
1.27-1.280.20171340.16242676X-RAY DIFFRACTION99.72
1.28-1.30.1941290.15992639X-RAY DIFFRACTION99.5
1.3-1.320.20941410.14832644X-RAY DIFFRACTION99.71
1.32-1.340.16551310.14132656X-RAY DIFFRACTION99.82
1.34-1.360.15581380.142677X-RAY DIFFRACTION99.72
1.36-1.380.19971480.14212614X-RAY DIFFRACTION99.86
1.38-1.410.1851340.14112698X-RAY DIFFRACTION99.82
1.41-1.430.17981190.14482675X-RAY DIFFRACTION99.93
1.43-1.460.19321430.13222614X-RAY DIFFRACTION99.96
1.46-1.490.15881300.12772714X-RAY DIFFRACTION99.96
1.49-1.520.16041260.12592643X-RAY DIFFRACTION100
1.52-1.560.1731400.12552689X-RAY DIFFRACTION100
1.56-1.60.17841510.1272688X-RAY DIFFRACTION100
1.6-1.640.17621390.12842646X-RAY DIFFRACTION100
1.64-1.690.17911660.1322649X-RAY DIFFRACTION100
1.69-1.740.15241430.12672699X-RAY DIFFRACTION100
1.74-1.810.15891350.12742671X-RAY DIFFRACTION100
1.81-1.880.16561510.13142670X-RAY DIFFRACTION100
1.88-1.960.16541480.13042710X-RAY DIFFRACTION100
1.96-2.070.15831330.12622716X-RAY DIFFRACTION99.89
2.07-2.20.14161550.12782667X-RAY DIFFRACTION99.86
2.2-2.370.17461400.13592734X-RAY DIFFRACTION99.97
2.37-2.60.1781680.14112696X-RAY DIFFRACTION99.93
2.6-2.980.1741580.14862732X-RAY DIFFRACTION100
2.98-3.750.1651480.12962753X-RAY DIFFRACTION99.21
3.75-25.960.17011510.15552920X-RAY DIFFRACTION99.64

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