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- PDB-5ghn: Crystal structure of human MTH1(G2K/D120N mutant) in complex with... -

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Basic information

Entry
Database: PDB / ID: 5ghn
TitleCrystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP
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 / 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 / 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
Chem-6U4 / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.391 Å
AuthorsNakamura, T. / Waz, S. / Hirata, K. / Nakabeppu, Y. / Yamagata, Y.
Citation
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.
#1: 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
DepositionJun 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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)37,1697
Polymers36,0852
Non-polymers1,0835
Water6,828379
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5964
Polymers18,0431
Non-polymers5533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area8400 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5733
Polymers18,0431
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.228, 47.271, 123.193
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 / 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: 18042.605 Da / Num. of mol.: 2 / Fragment: UNP residues 42-197 / Mutation: G2K, D120N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Plasmid: pET8c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 1.87 Å3/Da / Density % sol: 34.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium citrate, Tris, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 53100 / % possible obs: 96.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 49.9
Reflection shellResolution: 1.39→1.41 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.391→31.001 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.23
RfactorNum. reflection% reflection
Rfree0.1889 2696 5.08 %
Rwork0.1487 --
obs0.1508 53051 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.391→31.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 65 379 2986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063002
X-RAY DIFFRACTIONf_angle_d0.9974116
X-RAY DIFFRACTIONf_dihedral_angle_d15.1221148
X-RAY DIFFRACTIONf_chiral_restr0.082419
X-RAY DIFFRACTIONf_plane_restr0.007544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3912-1.41650.24421490.16492508X-RAY DIFFRACTION93
1.4165-1.44370.19841310.15122599X-RAY DIFFRACTION95
1.4437-1.47320.2231480.14752554X-RAY DIFFRACTION95
1.4732-1.50520.20191300.14082598X-RAY DIFFRACTION95
1.5052-1.54020.20651320.14222594X-RAY DIFFRACTION95
1.5402-1.57870.21311410.13772575X-RAY DIFFRACTION95
1.5787-1.62140.21531400.13772615X-RAY DIFFRACTION96
1.6214-1.66910.21061350.1412601X-RAY DIFFRACTION96
1.6691-1.7230.20371340.13962636X-RAY DIFFRACTION96
1.723-1.78460.17671290.14122662X-RAY DIFFRACTION96
1.7846-1.8560.18071530.13992616X-RAY DIFFRACTION97
1.856-1.94050.16171740.13432622X-RAY DIFFRACTION97
1.9405-2.04280.18421510.13342648X-RAY DIFFRACTION97
2.0428-2.17070.19191270.13972691X-RAY DIFFRACTION97
2.1707-2.33830.18781510.1482698X-RAY DIFFRACTION98
2.3383-2.57350.20961470.16392721X-RAY DIFFRACTION98
2.5735-2.94560.19511350.16392761X-RAY DIFFRACTION98
2.9456-3.71020.15261480.14472781X-RAY DIFFRACTION99
3.7102-31.00830.19581410.16062875X-RAY DIFFRACTION96

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