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- PDB-5ghp: Crystal structure of human MTH1(G2K/D120A mutant) in complex with... -

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Basic information

Entry
Database: PDB / ID: 5ghp
TitleCrystal structure of human MTH1(G2K/D120A 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 / 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 / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.192 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)36,0454
Polymers35,9992
Non-polymers462
Water7,638424
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0232
Polymers18,0001
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area8440 Å2
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0232
Polymers18,0001
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.233, 47.237, 123.195
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: 17999.580 Da / Num. of mol.: 2 / Fragment: UNP residues 42-197 / Mutation: G2K, D120A
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 34.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Sodium citrate, Sodium cacodylate, 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: 1.19→50 Å / Num. obs: 86636 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 37.2
Reflection shellResolution: 1.19→1.21 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: 1.192→43.285 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.94
RfactorNum. reflection% reflection
Rfree0.1789 4327 5 %
Rwork0.1469 --
obs0.1485 86548 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.192→43.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 2 424 2962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072867
X-RAY DIFFRACTIONf_angle_d0.9793904
X-RAY DIFFRACTIONf_dihedral_angle_d14.2771092
X-RAY DIFFRACTIONf_chiral_restr0.083409
X-RAY DIFFRACTIONf_plane_restr0.008517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1925-1.2060.25091330.19562554X-RAY DIFFRACTION93
1.206-1.22020.20621280.17792741X-RAY DIFFRACTION100
1.2202-1.23510.22071250.17162705X-RAY DIFFRACTION100
1.2351-1.25070.20831390.16472734X-RAY DIFFRACTION100
1.2507-1.26720.22821500.1622689X-RAY DIFFRACTION100
1.2672-1.28460.20091530.15662736X-RAY DIFFRACTION100
1.2846-1.30290.17471530.15022658X-RAY DIFFRACTION100
1.3029-1.32240.1821550.1422737X-RAY DIFFRACTION100
1.3224-1.3430.18951440.13872714X-RAY DIFFRACTION100
1.343-1.3650.20351450.14382727X-RAY DIFFRACTION100
1.365-1.38860.17171440.13472722X-RAY DIFFRACTION100
1.3886-1.41380.15661630.13532680X-RAY DIFFRACTION100
1.4138-1.4410.17561570.13532735X-RAY DIFFRACTION100
1.441-1.47040.18081410.12822714X-RAY DIFFRACTION100
1.4704-1.50240.18481450.12872741X-RAY DIFFRACTION100
1.5024-1.53740.16991610.12222713X-RAY DIFFRACTION100
1.5374-1.57580.16151280.11872758X-RAY DIFFRACTION100
1.5758-1.61840.17381390.12122716X-RAY DIFFRACTION100
1.6184-1.66610.17961280.12112753X-RAY DIFFRACTION100
1.6661-1.71980.17221300.12922755X-RAY DIFFRACTION100
1.7198-1.78130.16451420.132760X-RAY DIFFRACTION100
1.7813-1.85260.1721530.1282751X-RAY DIFFRACTION100
1.8526-1.93690.16371370.12942754X-RAY DIFFRACTION100
1.9369-2.03910.14981410.12922758X-RAY DIFFRACTION100
2.0391-2.16680.15111450.13292767X-RAY DIFFRACTION100
2.1668-2.33410.15271490.14142781X-RAY DIFFRACTION100
2.3341-2.5690.18151420.16092809X-RAY DIFFRACTION100
2.569-2.94060.20961480.17092806X-RAY DIFFRACTION100
2.9406-3.70460.15331610.1482824X-RAY DIFFRACTION100
3.7046-43.31380.2221480.17352929X-RAY DIFFRACTION98

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