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- PDB-8i19: Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo... -

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Basic information

Entry
Database: PDB / ID: 8i19
TitleCrystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP at pH 8.0
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / Nudix 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.48 Å
AuthorsNakamura, T. / Yamagata, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Febs Lett. / Year: 2023
Title: Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition.
Authors: Nakamura, T. / Koga-Ogawa, Y. / Fujimiya, K. / Chirifu, M. / Goto, M. / Ikemizu, S. / Nakabeppu, Y. / Yamagata, Y.
History
DepositionJan 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)37,2489
Polymers36,0872
Non-polymers1,1617
Water6,864381
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6365
Polymers18,0441
Non-polymers5924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area8170 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6134
Polymers18,0441
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.498, 47.993, 123.489
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.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.87 Å3/Da / Density % sol: 34.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, tris, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.48→36.63 Å / Num. obs: 45875 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 10.66 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 39.8
Reflection shellResolution: 1.48→1.51 Å / Rmerge(I) obs: 0.268 / Num. unique obs: 2237

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5GHI

5ghi


Resolution: 1.48→36.63 Å / SU ML: 0.1427 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.4406 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1901 2323 5.07 %
Rwork0.1505 43500 -
obs0.1525 45823 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.99 Å2
Refinement stepCycle: LAST / Resolution: 1.48→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 69 381 2992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532933
X-RAY DIFFRACTIONf_angle_d1.10764010
X-RAY DIFFRACTIONf_chiral_restr0.0745408
X-RAY DIFFRACTIONf_plane_restr0.0061522
X-RAY DIFFRACTIONf_dihedral_angle_d16.20341108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.22141310.14622435X-RAY DIFFRACTION95.53
1.51-1.540.21781400.13832490X-RAY DIFFRACTION98.98
1.54-1.580.22261370.14032504X-RAY DIFFRACTION98.99
1.58-1.620.23621260.1332519X-RAY DIFFRACTION99.1
1.62-1.660.21221220.1362549X-RAY DIFFRACTION99.18
1.66-1.710.19251450.13352509X-RAY DIFFRACTION99.36
1.71-1.760.20471350.13082520X-RAY DIFFRACTION99.29
1.76-1.830.19061370.12812564X-RAY DIFFRACTION99.48
1.83-1.90.17821430.12642532X-RAY DIFFRACTION99.59
1.9-1.990.19231250.12862574X-RAY DIFFRACTION99.78
1.99-2.090.16571560.13742543X-RAY DIFFRACTION99.82
2.09-2.220.20461350.13942555X-RAY DIFFRACTION99.96
2.22-2.390.16991330.15652605X-RAY DIFFRACTION99.89
2.39-2.630.23671310.16972603X-RAY DIFFRACTION99.96
2.63-3.020.17581280.18022629X-RAY DIFFRACTION99.93
3.02-3.80.18891490.15232618X-RAY DIFFRACTION99.71
3.8-36.630.17081500.16792751X-RAY DIFFRACTION99.15

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