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- PDB-6ijy: Crystal structure of human MTH1(G2K/C87A/C104S mutant) in complex... -

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Basic information

Entry
Database: PDB / ID: 6ijy
TitleCrystal structure of human MTH1(G2K/C87A/C104S mutant) in complex with 8-oxo-dGTP determined using a crystal obtained under microgravity
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / ALPHA-BETA-ALPHA SANDWICH / DNA DAMAGE / DNA REPAIR / DNA REPLICATION
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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ...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 / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / DNA protection / Phosphate bond hydrolysis by NUDT proteins / 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 / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Oxidized purine nucleoside triphosphate / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
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: 1.04 Å
AuthorsNakamura, T. / Yamagata, Y.
Citation
Journal: Int. J. Microgravity Sci. Appl. / Year: 2019
Title: X-ray Structure Analysis of Human Oxidized Nucleotide Hydrolase MTH1 using Crystals Obtained under Microgravity.
Authors: Nakamura, T. / Hirata, K. / Fujimiya, K. / Chirifu, M. / Arimori, T. / Tamada, T. / Ikemizu, S. / Yamagata, Y.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity.
Authors: Waz, S. / Nakamura, T. / Hirata, K. / Koga-Ogawa, Y. / Chirifu, M. / Arimori, T. / Tamada, T. / Ikemizu, S. / Nakabeppu, Y. / Yamagata, Y.
#2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization and preliminary X-ray analysis of human MTH1 with a homogeneous N-terminus.
Authors: Koga, Y. / Inazato, M. / Nakamura, T. / Hashikawa, C. / Chirifu, M. / Michi, A. / Yamashita, T. / Toma, S. / Kuniyasu, A. / Ikemizu, S. / Nakabeppu, Y. / Yamagata, Y.
History
DepositionOct 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)37,31310
Polymers35,9912
Non-polymers1,3238
Water5,837324
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7727
Polymers17,9951
Non-polymers7766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area8160 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 area0 Å2
ΔGint0 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.492, 48.099, 123.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Mutation: G2K,C87A,C104S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 293 K / Method: counter-diffusion
Details: sodium citrate, cacodylate, sodium chloride, glycerol

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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 MX300HE / Detector: CCD / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 131109 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 65.7
Reflection shellResolution: 1.04→1.06 Å / Rmerge(I) obs: 0.9 / Num. unique obs: 6458

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.04→37.996 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.48
RfactorNum. reflection% reflection
Rfree0.1583 6595 5.03 %
Rwork0.1334 --
obs0.1346 131001 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.04→37.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 80 324 2944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083150
X-RAY DIFFRACTIONf_angle_d1.3764326
X-RAY DIFFRACTIONf_dihedral_angle_d16.5741193
X-RAY DIFFRACTIONf_chiral_restr0.081439
X-RAY DIFFRACTIONf_plane_restr0.009561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0397-1.05150.29671920.24983927X-RAY DIFFRACTION96
1.0515-1.06390.19882350.18114085X-RAY DIFFRACTION100
1.0639-1.07690.18382230.1534049X-RAY DIFFRACTION100
1.0769-1.09050.15332320.13644148X-RAY DIFFRACTION100
1.0905-1.10490.1472180.12984114X-RAY DIFFRACTION100
1.1049-1.120.15522240.12694130X-RAY DIFFRACTION100
1.12-1.1360.1472150.11874086X-RAY DIFFRACTION100
1.136-1.1530.14272470.11524046X-RAY DIFFRACTION100
1.153-1.1710.12642230.11314161X-RAY DIFFRACTION100
1.171-1.19020.1322060.10914092X-RAY DIFFRACTION100
1.1902-1.21070.12552180.10984152X-RAY DIFFRACTION100
1.2107-1.23270.13072320.10624099X-RAY DIFFRACTION100
1.2327-1.25640.1441930.10824144X-RAY DIFFRACTION100
1.2564-1.28210.13892070.10724127X-RAY DIFFRACTION100
1.2821-1.310.13712230.10784134X-RAY DIFFRACTION100
1.31-1.34040.13952120.10664166X-RAY DIFFRACTION100
1.3404-1.3740.12792260.10554139X-RAY DIFFRACTION100
1.374-1.41110.1391970.10634131X-RAY DIFFRACTION100
1.4111-1.45260.1292000.10574164X-RAY DIFFRACTION100
1.4526-1.49950.13892170.10744147X-RAY DIFFRACTION100
1.4995-1.55310.13982340.10724137X-RAY DIFFRACTION100
1.5531-1.61530.14652080.11084194X-RAY DIFFRACTION100
1.6153-1.68880.14352380.11544147X-RAY DIFFRACTION100
1.6888-1.77790.14672020.11874190X-RAY DIFFRACTION100
1.7779-1.88920.13812220.1194171X-RAY DIFFRACTION100
1.8892-2.03510.13782440.12214163X-RAY DIFFRACTION100
2.0351-2.23990.13862140.12734228X-RAY DIFFRACTION100
2.2399-2.56390.16052160.14164255X-RAY DIFFRACTION100
2.5639-3.230.20112450.15614270X-RAY DIFFRACTION100
3.23-38.02160.18472320.16494410X-RAY DIFFRACTION99

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