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- PDB-5otn: Crystal structure of zebrafish MTH1 in complex with O6-methyl-dGMP -

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Basic information

Entry
Database: PDB / ID: 5otn
TitleCrystal structure of zebrafish MTH1 in complex with O6-methyl-dGMP
ComponentsNudix (Nucleoside diphosphate linked moiety X)-type motif 1
KeywordsHYDROLASE / MTH1 / Inhibitor / Complex / NUDIX / Methylated nucleotide / O6-methyl-dGMP / zebrafish
Function / homology
Function and homology information


purine deoxyribonucleotide metabolic process / Phosphate bond hydrolysis by NUDT proteins / nucleoside triphosphate diphosphatase activity / 2-hydroxy-dATP diphosphatase / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / phosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mitochondrial matrix ...purine deoxyribonucleotide metabolic process / Phosphate bond hydrolysis by NUDT proteins / nucleoside triphosphate diphosphatase activity / 2-hydroxy-dATP diphosphatase / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / phosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mitochondrial matrix / RNA binding / 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 / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Nudix (Nucleoside diphosphate linked moiety X)-type motif 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,85918
Polymers18,3271
Non-polymers1,53217
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-36 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.528, 55.379, 65.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nudix (Nucleoside diphosphate linked moiety X)-type motif 1 / Nudix (nucleoside diphosphate-linked moiety X)-type motif 1


Mass: 18326.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: nudt1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7ZWC3

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Non-polymers , 6 types, 180 molecules

#2: Chemical ChemComp-6OG / 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 361.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.2 M CaCl2, 0.1 M MES pH 6.0, 20% (w/v) PEG6000, 2.5 mM O6-methyl-2'-dGTP, 6 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 0.99→28.32 Å / Num. obs: 90549 / % possible obs: 99.2 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.1
Reflection shellResolution: 0.99→1.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4198 / CC1/2: 0.418 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HZX

5hzx


Resolution: 0.99→28.32 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.556 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.018 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13331 2217 2.5 %RANDOM
Rwork0.12078 ---
obs0.1211 88256 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.181 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 0.99→28.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 94 163 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191534
X-RAY DIFFRACTIONr_bond_other_d0.0020.021443
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9992068
X-RAY DIFFRACTIONr_angle_other_deg0.91333362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8455186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55824.30672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7615274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.924159
X-RAY DIFFRACTIONr_chiral_restr0.1050.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021698
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02320
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_it0.8390.837702
X-RAY DIFFRACTIONr_mcbond_other0.8340.834701
X-RAY DIFFRACTIONr_mcangle_it1.1131.266902
X-RAY DIFFRACTIONr_mcangle_other1.1131.27903
X-RAY DIFFRACTIONr_scbond_it1.3711.152832
X-RAY DIFFRACTIONr_scbond_other1.3681.152832
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6471.6181167
X-RAY DIFFRACTIONr_long_range_B_refined2.40410.8261531
X-RAY DIFFRACTIONr_long_range_B_other2.40410.8431532
X-RAY DIFFRACTIONr_rigid_bond_restr1.26332977
X-RAY DIFFRACTIONr_sphericity_free23.2715106
X-RAY DIFFRACTIONr_sphericity_bonded5.89953002
LS refinement shellResolution: 0.99→1.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 146 -
Rwork0.296 6133 -
obs--94.45 %

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