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- PDB-9mbn: 2-Oxo-dATP hydrolysis in human MTH1(G2K mutant) crystal using Mn2... -

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Basic information

Entry
Database: PDB / ID: 9mbn
Title2-Oxo-dATP hydrolysis in human MTH1(G2K mutant) crystal using Mn2+: the EP-M 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 / cytosol / cytoplasm
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
2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE / : / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 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)37,11110
Polymers36,0872
Non-polymers1,0248
Water5,837324
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5565
Polymers18,0441
Non-polymers5124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-9 kcal/mol
Surface area8280 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5565
Polymers18,0441
Non-polymers5124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-9 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.488, 47.595, 124.060
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-IGU / 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 35.32 %
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: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→33.26 Å / Num. obs: 40279 / % possible obs: 98.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.61 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 26.9
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.459 / Num. unique obs: 1983

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→33.26 Å / SU ML: 0.1505 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.035 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2074 2010 5 %
Rwork0.1699 38220 -
obs0.1718 40230 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.18 Å2
Refinement stepCycle: LAST / Resolution: 1.55→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 52 324 2918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542783
X-RAY DIFFRACTIONf_angle_d0.86673786
X-RAY DIFFRACTIONf_chiral_restr0.0558386
X-RAY DIFFRACTIONf_plane_restr0.0066497
X-RAY DIFFRACTIONf_dihedral_angle_d15.31471049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.26131480.22682626X-RAY DIFFRACTION97.61
1.59-1.630.2321460.21142706X-RAY DIFFRACTION99.17
1.63-1.680.29951510.21062677X-RAY DIFFRACTION99.26
1.68-1.730.25051340.20632709X-RAY DIFFRACTION99.09
1.73-1.80.21691440.18962720X-RAY DIFFRACTION98.83
1.8-1.870.22531570.18222676X-RAY DIFFRACTION99.09
1.87-1.950.21151500.1712724X-RAY DIFFRACTION99.52
1.95-2.060.19131480.17172719X-RAY DIFFRACTION99.24
2.06-2.190.23171410.16982731X-RAY DIFFRACTION99.41
2.19-2.350.22281360.17492762X-RAY DIFFRACTION99.49
2.35-2.590.23271310.18532794X-RAY DIFFRACTION99.69
2.59-2.970.22231350.18162777X-RAY DIFFRACTION98.98
2.97-3.740.1841310.14562767X-RAY DIFFRACTION97.54
3.74-33.260.17591580.15282832X-RAY DIFFRACTION95.53

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