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- PDB-9mbe: Neutron crystal structure of human MTH1(G2K/C87A/C104S mutant) in... -

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Basic information

Entry
Database: PDB / ID: 9mbe
TitleNeutron crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 8-oxo-dGTP
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 cadmium ion / acrosomal vesicle / male gonad development / nuclear membrane / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / extracellular space / 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
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsFujimiya, K. / Hirata, K. / Ostermann, A. / Schrader, T.E. / Hiromoto, T. / Arimori, T. / Hirano, Y. / Tamada, T. / 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)37,1067
Polymers35,9912
Non-polymers1,1155
Water5,405300
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5654
Polymers17,9951
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area8260 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5423
Polymers17,9951
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.850, 48.160, 124.100
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 / 2-hydroxy-dATP diphosphatase / 8-oxo-dGTPase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 17995.459 Da / Num. of mol.: 2
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.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: sodium citrate, cacodylate, NaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NE3A11
NUCLEAR REACTORFRM II BIODIFF23.1
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M1PIXELDec 16, 2018
BIODIFF2IMAGE PLATEMay 29, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
23.11
Reflection

Biso Wilson estimate: 10.02 Å2 / Entry-ID: 9MBE

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.4-32.085382297.86.60.042126.7
1.7-38.052629183.72.60.14225.5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsDiffraction-ID
1.4-1.440.20338461
1.7-1.750.38719452

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Processing

Software
NameClassification
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction
XDSdata scaling
Refinement

SU ML: 0.131 / Cross valid method: FREE R-VALUE / Method to determine structure: FOURIER SYNTHESIS / Phase error: 19.3669 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: GeoStd + Monomer Library / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.4-32.08X-RAY DIFFRACTION20.430.19690.17410.1752268851129538174.9997.811.35
1.7-38.05NEUTRON DIFFRACTION0.23970.215313182626783.462
Refinement stepCycle: LAST / Resolution: 1.4→32.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 67 300 2907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01045940
X-RAY DIFFRACTIONf_angle_d1.57310618
X-RAY DIFFRACTIONf_chiral_restr0.0943391
X-RAY DIFFRACTIONf_plane_restr0.00731128
X-RAY DIFFRACTIONf_dihedral_angle_d18.18761667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.23711460.22372602X-RAY DIFFRACTION95.95
1.43-1.450.2751280.21022606X-RAY DIFFRACTION96.4
1.45-1.480.22481280.20822633X-RAY DIFFRACTION96.44
1.48-1.510.24511490.20382612X-RAY DIFFRACTION96.57
1.51-1.550.18561380.19292622X-RAY DIFFRACTION96.81
1.55-1.590.24021350.19652644X-RAY DIFFRACTION97.03
1.59-1.630.2191310.18542639X-RAY DIFFRACTION97.23
1.63-1.680.20211390.1872654X-RAY DIFFRACTION97.56
1.68-1.730.22651470.18232649X-RAY DIFFRACTION97.66
1.73-1.80.20661450.17932686X-RAY DIFFRACTION97.89
1.8-1.870.18721360.18072666X-RAY DIFFRACTION98.07
1.87-1.950.21171440.17052702X-RAY DIFFRACTION98.31
1.95-2.060.21831480.16882691X-RAY DIFFRACTION98.47
2.06-2.180.17551450.16362739X-RAY DIFFRACTION98.46
2.18-2.350.19931360.16472680X-RAY DIFFRACTION98.02
2.35-2.590.18221400.17182757X-RAY DIFFRACTION98.98
2.59-2.960.19961410.17292785X-RAY DIFFRACTION99.15
2.96-3.730.16871500.15512817X-RAY DIFFRACTION99.63
3.73-32.080.17811620.16742945X-RAY DIFFRACTION99.42
1.7-1.760.34970.29952428NEUTRON DIFFRACTION

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