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- PDB-7ayz: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 7ayz
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with activator TH10785
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / 8-oxoguanine DNA glycosylase / N-glycosylase / DNA lyase / DNA repair
Function / homology
Function and homology information


Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity ...Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / positive regulation of gene expression via chromosomal CpG island demethylation / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to reactive oxygen species / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / response to oxidative stress / microtubule binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / DNA damage response / regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus
Similarity search - Function
8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / : / 8-oxoguanine DNA glycosylase, N-terminal domain / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
NICKEL (II) ION / ~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMasuyer, G. / Davies, J.R. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Science / Year: 2022
Title: Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function.
Authors: Michel, M. / Benitez-Buelga, C. / Calvo, P.A. / Hanna, B.M.F. / Mortusewicz, O. / Masuyer, G. / Davies, J. / Wallner, O. / Sanjiv, K. / Albers, J.J. / Castaneda-Zegarra, S. / Jemth, A.S. / ...Authors: Michel, M. / Benitez-Buelga, C. / Calvo, P.A. / Hanna, B.M.F. / Mortusewicz, O. / Masuyer, G. / Davies, J. / Wallner, O. / Sanjiv, K. / Albers, J.J. / Castaneda-Zegarra, S. / Jemth, A.S. / Visnes, T. / Sastre-Perona, A. / Danda, A.N. / Homan, E.J. / Marimuthu, K. / Zhenjun, Z. / Chi, C.N. / Sarno, A. / Wiita, E. / von Nicolai, C. / Komor, A.J. / Rajagopal, V. / Muller, S. / Hank, E.C. / Varga, M. / Scaletti, E.R. / Pandey, M. / Karsten, S. / Haslene-Hox, H. / Loevenich, S. / Marttila, P. / Rasti, A. / Mamonov, K. / Ortis, F. / Schomberg, F. / Loseva, O. / Stewart, J. / D'Arcy-Evans, N. / Koolmeister, T. / Henriksson, M. / Michel, D. / de Ory, A. / Acero, L. / Calvete, O. / Scobie, M. / Hertweck, C. / Vilotijevic, I. / Kalderen, C. / Osorio, A. / Perona, R. / Stolz, A. / Stenmark, P. / Berglund, U.W. / de Vega, M. / Helleday, T.
History
DepositionNov 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: N-glycosylase/DNA lyase
BBB: N-glycosylase/DNA lyase
CCC: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,3117
Polymers107,4503
Non-polymers8614
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mOGG1 is a monomer in solution when purified by size exclusion
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-17 kcal/mol
Surface area42400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.833, 81.802, 170.643
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-glycosylase/DNA lyase


Mass: 35816.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Truncated mouse OGG1 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ogg1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O08760, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-SEQ / ~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine / TH10785


Mass: 267.369 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.06 M Divalents, 0.1 M Buffer System 3 pH 8.5, 30 % v/v Precipitant Mix 2 (Morpheus screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→85.3 Å / Num. obs: 35633 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Net I/σ(I): 18.3
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4269 / CC1/2: 0.87 / Rpim(I) all: 0.412 / Rrim(I) all: 1.07

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3Y

6g3y


Resolution: 2.6→73.873 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.839 / SU ML: 0.288 / Cross valid method: FREE R-VALUE / ESU R: 0.897 / ESU R Free: 0.358
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2861 1850 5.204 %
Rwork0.2368 33700 -
all0.239 --
obs-35550 99.944 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 73.594 Å2
Baniso -1Baniso -2Baniso -3
1--2.627 Å20 Å20 Å2
2--5.572 Å20 Å2
3----2.945 Å2
Refinement stepCycle: LAST / Resolution: 2.6→73.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7381 0 61 67 7509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0137656
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176883
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.64710428
X-RAY DIFFRACTIONr_angle_other_deg1.0841.58315924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.73721.244418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6041559
X-RAY DIFFRACTIONr_chiral_restr0.0430.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021723
X-RAY DIFFRACTIONr_nbd_refined0.1780.21489
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.26338
X-RAY DIFFRACTIONr_nbtor_refined0.1550.23575
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23142
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2172
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.227
X-RAY DIFFRACTIONr_nbd_other0.2360.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.24
X-RAY DIFFRACTIONr_mcbond_it3.2028.0133729
X-RAY DIFFRACTIONr_mcbond_other3.28.0133728
X-RAY DIFFRACTIONr_mcangle_it5.32712.0064649
X-RAY DIFFRACTIONr_mcangle_other5.32612.0074650
X-RAY DIFFRACTIONr_scbond_it2.6568.0423927
X-RAY DIFFRACTIONr_scbond_other2.6568.0423928
X-RAY DIFFRACTIONr_scangle_it4.50411.9885770
X-RAY DIFFRACTIONr_scangle_other4.50311.9885771
X-RAY DIFFRACTIONr_lrange_it7.88889.6118429
X-RAY DIFFRACTIONr_lrange_other7.88889.6168429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6670.4071430.3762435X-RAY DIFFRACTION99.8451
2.667-2.7410.3451420.3392396X-RAY DIFFRACTION99.9213
2.741-2.820.3461640.3132279X-RAY DIFFRACTION99.9182
2.82-2.9070.4011100.2782274X-RAY DIFFRACTION99.7907
2.907-3.0020.2921080.2792197X-RAY DIFFRACTION100
3.002-3.1070.2991100.2842141X-RAY DIFFRACTION99.9556
3.107-3.2240.3791060.2952046X-RAY DIFFRACTION99.9536
3.224-3.3560.3161140.2681973X-RAY DIFFRACTION99.9043
3.356-3.5050.303870.2551932X-RAY DIFFRACTION99.9505
3.505-3.6750.296920.2471831X-RAY DIFFRACTION100
3.675-3.8740.261270.2411707X-RAY DIFFRACTION100
3.874-4.1080.243840.2181670X-RAY DIFFRACTION100
4.108-4.3910.242830.2091541X-RAY DIFFRACTION100
4.391-4.7420.219520.2011492X-RAY DIFFRACTION100
4.742-5.1930.312840.2061328X-RAY DIFFRACTION100
5.193-5.8030.272620.2191230X-RAY DIFFRACTION100
5.803-6.6960.329690.2321083X-RAY DIFFRACTION100
6.696-8.1880.27520.204952X-RAY DIFFRACTION100
8.188-11.5260.232410.163739X-RAY DIFFRACTION100

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