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- PDB-5otm: Crystal structure of human MTH1 in complex with O6-methyl-dGMP -

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Basic information

Entry
Database: PDB / ID: 5otm
TitleCrystal structure of human MTH1 in complex with O6-methyl-dGMP
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / MTH1 / Inhibitor / Complex / NUDIX / Methylated nucleotide / O6-methyl-dGMP
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
6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE / ACETATE ION / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGustafsson, R. / Henriksson, L. / Jemth, A.-S. / Brautigam, L. / Carreras Puigvert, J. / Homan, E. / Warpman Berglund, U. / Helleday, T. / Stenmark, P.
Funding support Sweden, 9items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
Wenner-Gren Foundation Sweden
Ake Wiberg Foundation Sweden
Swedish Foundation for Strategic Research Sweden
Swedish Pain Relief Foundation Sweden
Torsten and Ragnar Soderberg Foundation Sweden
Swedish Childrens Cancer Foundation Sweden
Swedish Cancer Society Sweden
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP.
Authors: Jemth, A.S. / Gustafsson, R. / Brautigam, L. / Henriksson, L. / Vallin, K.S.A. / Sarno, A. / Almlof, I. / Homan, E. / Rasti, A. / Warpman Berglund, U. / Stenmark, P. / Helleday, T.
History
DepositionAug 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 28, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,05813
Polymers36,5072
Non-polymers1,55011
Water4,360242
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0587
Polymers18,2541
Non-polymers8056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9996
Polymers18,2541
Non-polymers7455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.581, 67.237, 79.025
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: 18253.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-6OG / 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 361.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N5O7P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 3.7
Details: 26% w/v PEG6000, 0.1 M Sodium acetate trihydrate pH 3.7, 0.2 M LiSO4, 3 mM O6-methyl-2'-dGTP, 2 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91801 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91801 Å / Relative weight: 1
ReflectionResolution: 1.8→47.57 Å / Num. obs: 29598 / % possible obs: 98.9 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1705 / CC1/2: 0.756 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZR1

3zr1


Resolution: 1.8→47.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.301 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24688 1487 5 %RANDOM
Rwork0.19612 ---
obs0.19861 28070 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.366 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---1.11 Å20 Å2
3---2.07 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2552 0 92 242 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192719
X-RAY DIFFRACTIONr_bond_other_d0.0010.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9883687
X-RAY DIFFRACTIONr_angle_other_deg0.82235626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5255316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39524.179134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4415456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8541516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02574
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2080.971265
X-RAY DIFFRACTIONr_mcbond_other0.2070.9681263
X-RAY DIFFRACTIONr_mcangle_it0.3571.451580
X-RAY DIFFRACTIONr_mcangle_other0.3571.451581
X-RAY DIFFRACTIONr_scbond_it0.3131.1361454
X-RAY DIFFRACTIONr_scbond_other0.3131.1381455
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4851.7012108
X-RAY DIFFRACTIONr_long_range_B_refined5.2612.3562952
X-RAY DIFFRACTIONr_long_range_B_other5.19211.8562905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 93 -
Rwork0.295 2007 -
obs--97.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3375-0.8048-0.46122.57672.06981.7062-0.00520.06970.1757-0.1790.0078-0.0046-0.1359-0.0276-0.00250.0271-0.0136-0.01530.04140.01450.0535-3.032-11.784-12.74
23.82910.20550.63916.24720.50230.14430.1194-0.58010.01960.4375-0.17550.48670.0618-0.11550.05610.1106-0.05330.04540.1254-0.02650.135-10.897-12.04-5.251
31.55210.1598-2.10075.3463-8.719616.71160.01920.08570.0657-0.01360.05960.1381-0.0413-0.2974-0.07890.1061-0.019-0.02780.0734-0.0430.19030.864-0.447-16.036
43.11341.40990.22143.74030.87650.5966-0.0116-0.1748-0.23420.2207-0.0543-0.14220.18130.07390.06590.06840.02440.01140.02950.03780.0641-0.193-19.195-9.8
54.55340.7567-2.02544.001-1.16276.7043-0.0859-0.2954-0.20210.1404-0.0823-0.19840.07990.22910.16820.01960.0002-0.04150.02350.03430.16188.907-5.292-10.459
65.964-1.6512-0.71385.25254.88228.6126-0.0265-0.4725-0.04840.1719-0.16580.28350.51170.06250.19230.0450.008300.0888-0.00790.118428.8168.672-7.01
76.5206-1.35161.76433.5363-0.28310.48330.0843-0.08350.5506-0.1133-0.203-0.25340.024-0.01170.11870.02860.00390.01830.0923-0.08990.186236.15213.597-7.4
85.47881.0684.30093.74982.121713.63810.15810.1164-0.0084-0.1555-0.0546-0.16080.31960.3322-0.10350.02610.0030.01540.0623-0.01760.195229.2444.224-12.672
95.29740.69241.11612.09071.20822.3277-0.0853-0.64571.0265-0.0093-0.0193-0.0227-0.1499-0.00570.10460.0172-0.00350.01360.0943-0.16870.392427.03219.989-4.822
105.52190.42450.18972.8874-0.98845.4350.2106-0.23170.1686-0.0469-0.09370.130.19940.084-0.11690.0152-0.0049-0.00060.0127-0.01440.097619.65.247-11.498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 42
2X-RAY DIFFRACTION2A43 - 65
3X-RAY DIFFRACTION3A66 - 82
4X-RAY DIFFRACTION4A83 - 118
5X-RAY DIFFRACTION5A119 - 156
6X-RAY DIFFRACTION6B0 - 18
7X-RAY DIFFRACTION7B19 - 62
8X-RAY DIFFRACTION8B63 - 87
9X-RAY DIFFRACTION9B88 - 120
10X-RAY DIFFRACTION10B121 - 156

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