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- PDB-6qvo: Crystal structure of human MTH1 in complex with N6-methyl-dAMP -

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Basic information

Entry
Database: PDB / ID: 6qvo
TitleCrystal structure of human MTH1 in complex with N6-methyl-dAMP
Components7,8-dihydro-8-oxoguanine triphosphatase
KeywordsHYDROLASE / ----
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
N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsScaletti, E. / Vallin, K.S. / Brautigam, L. / Sarno, A. / Warpman Berglund, U. / Helleday, T. / Stenmark, P. / Jemth, A.S.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool.
Authors: Scaletti, E.R. / Vallin, K.S. / Brautigam, L. / Sarno, A. / Warpman Berglund, U. / Helleday, T. / Stenmark, P. / Jemth, A.S.
History
DepositionMar 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
C: 7,8-dihydro-8-oxoguanine triphosphatase
D: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,22415
Polymers90,1744
Non-polymers2,04911
Water1,56787
1
A: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1775
Polymers22,5441
Non-polymers6334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0774
Polymers22,5441
Non-polymers5333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0814
Polymers22,5441
Non-polymers5373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 7,8-dihydro-8-oxoguanine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8892
Polymers22,5441
Non-polymers3451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.478, 67.111, 117.678
Angle α, β, γ (deg.)90.00, 94.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA3 - 15244 - 193
21GLUGLUBB3 - 15244 - 193
12THRTHRAA3 - 15544 - 196
22THRTHRCC3 - 15544 - 196
13VALVALAA3 - 15344 - 194
23VALVALDD3 - 15344 - 194
14GLUGLUBB3 - 15244 - 193
24GLUGLUCC3 - 15244 - 193
15GLUGLUBB3 - 15244 - 193
25GLUGLUDD3 - 15244 - 193
16VALVALCC3 - 15344 - 194
26VALVALDD3 - 15344 - 194

NCS ensembles :
ID
6
1
2
3
4
5

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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: 22543.566 Da / Num. of mol.: 4
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-6MA / N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 345.248 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H16N5O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium acetate pH 3.5, 26 % PEG3350, 0.2 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.45→58.6 Å / Num. obs: 20436 / % possible obs: 100 % / Redundancy: 6.9 % / Net I/σ(I): 3.2
Reflection shellResolution: 2.45→2.55 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→58.6 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 20.439 / SU ML: 0.411 / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 971 4.8 %RANDOM
Rwork0.23765 ---
obs0.23999 19444 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.268 Å2
Baniso -1Baniso -2Baniso -3
1-9.64 Å20 Å20.89 Å2
2---2.34 Å20 Å2
3----7.34 Å2
Refinement stepCycle: LAST / Resolution: 2.45→58.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 0 128 87 5144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195193
X-RAY DIFFRACTIONr_bond_other_d0.0010.024649
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.987040
X-RAY DIFFRACTIONr_angle_other_deg0.84310790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0485610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66724.353255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47415856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.391528
X-RAY DIFFRACTIONr_chiral_restr0.0750.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021114
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_it2.5085.6692449
X-RAY DIFFRACTIONr_mcbond_other2.5085.6682448
X-RAY DIFFRACTIONr_mcangle_it4.2928.4953056
X-RAY DIFFRACTIONr_mcangle_other4.2928.4973057
X-RAY DIFFRACTIONr_scbond_it2.225.8432744
X-RAY DIFFRACTIONr_scbond_other2.225.8432745
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8148.6823985
X-RAY DIFFRACTIONr_long_range_B_refined6.94661.2565383
X-RAY DIFFRACTIONr_long_range_B_other6.94661.2535384
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A93040.05
12B93040.05
21A95220.04
22C95220.04
31A92620.05
32D92620.05
41B94060.05
42C94060.05
51B92860.05
52D92860.05
61C93580.04
62D93580.04
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 67 -
Rwork0.389 1449 -
obs--99.93 %

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