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

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Basic information

Entry
Database: PDB / ID: 9mbl
Title2-Oxo-dATP hydrolysis in human MTH1(G2K mutant) crystal using Mn2+: the ES-2M 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
Chem-6U4 / : / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.37 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)37,41312
Polymers36,0872
Non-polymers1,32610
Water7,368409
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7076
Polymers18,0441
Non-polymers6635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-35 kcal/mol
Surface area7980 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7076
Polymers18,0441
Non-polymers6635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-37 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.503, 47.357, 123.631
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-6U4 / [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate / 2-oxo-dATP


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 1.89 Å3/Da / Density % sol: 34.79 %
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: 1.37→44.22 Å / Num. obs: 57873 / % possible obs: 100 % / Redundancy: 5.6 % / Biso Wilson estimate: 12.92 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.6
Reflection shellResolution: 1.37→1.39 Å / Rmerge(I) obs: 0.295 / Num. unique obs: 2845

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.37→44.22 Å / SU ML: 0.133 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 15.2485 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.181 2934 5.08 %
Rwork0.1337 54854 -
obs0.1361 57788 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.71 Å2
Refinement stepCycle: LAST / Resolution: 1.37→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 70 409 3021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053118
X-RAY DIFFRACTIONf_angle_d0.96864242
X-RAY DIFFRACTIONf_chiral_restr0.0739422
X-RAY DIFFRACTIONf_plane_restr0.0058553
X-RAY DIFFRACTIONf_dihedral_angle_d17.14991202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.22521230.17662473X-RAY DIFFRACTION95.62
1.4-1.420.24321510.1662540X-RAY DIFFRACTION99.85
1.42-1.450.22991410.14962618X-RAY DIFFRACTION100
1.45-1.470.22571570.14172541X-RAY DIFFRACTION99.96
1.47-1.50.19411420.13272586X-RAY DIFFRACTION99.93
1.5-1.540.19441480.12472571X-RAY DIFFRACTION100
1.54-1.570.17791520.1292563X-RAY DIFFRACTION99.78
1.57-1.610.1781370.12242586X-RAY DIFFRACTION99.96
1.61-1.650.16551430.12262612X-RAY DIFFRACTION100
1.65-1.70.18851330.12092592X-RAY DIFFRACTION100
1.7-1.760.19841300.122607X-RAY DIFFRACTION100
1.76-1.820.18771360.12092593X-RAY DIFFRACTION99.85
1.82-1.890.19061310.12292628X-RAY DIFFRACTION99.96
1.89-1.980.15541300.12162609X-RAY DIFFRACTION100
1.98-2.080.16331490.12382598X-RAY DIFFRACTION100
2.08-2.210.18381360.12692646X-RAY DIFFRACTION99.96
2.21-2.390.15921420.13372623X-RAY DIFFRACTION100
2.39-2.630.16881490.1452644X-RAY DIFFRACTION100
2.63-3.010.19261370.14442671X-RAY DIFFRACTION99.96
3.01-3.790.17121230.12642712X-RAY DIFFRACTION100
3.79-44.220.18391440.14622841X-RAY DIFFRACTION99.8

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