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- PDB-7ayy: Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 7ayy
TitleStructure of the human 8-oxoguanine DNA Glycosylase hOGG1 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


Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 ...Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / response to light stimulus / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cellular response to cadmium ion / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / cellular response to reactive oxygen species / response to estradiol / microtubule binding / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / mitochondrial matrix / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol
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
~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
DDD: N-glycosylase/DNA lyase
EEE: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,71615
Polymers189,6095
Non-polymers2,10710
Water12,683704
1
AAA: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • Evidence: gel filtration, hOGG1 is a monomer in solution when purified by size exclusion
  • 38.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)38,3843
Polymers37,9221
Non-polymers4632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • 38.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)38,3843
Polymers37,9221
Non-polymers4632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • 38.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)38,1892
Polymers37,9221
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • 38.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)38,2813
Polymers37,9221
Non-polymers3592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
EEE: N-glycosylase/DNA lyase
hetero molecules


  • defined by author
  • 38.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)38,4774
Polymers37,9221
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.025, 86.025, 427.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
N-glycosylase/DNA lyase


Mass: 37921.879 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Truncated version of hOGG1 / Source: (gene. exp.) Homo sapiens (human) / Gene: OGG1, MMH, MUTM, OGH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O15527, 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.: 5 / Source method: obtained synthetically / Formula: C17H21N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5 and 48 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2→86.03 Å / Num. obs: 110134 / % possible obs: 100 % / Redundancy: 24.1 % / Biso Wilson estimate: 22.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.087 / Rrim(I) all: 0.311 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 19 % / Rmerge(I) obs: 2.65 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5306 / CC1/2: 0.529 / Rpim(I) all: 0.886 / Rrim(I) all: 2.79 / % possible all: 100

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Processing

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

6rlw


Resolution: 2→84.478 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.496 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.21 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2503 5445 4.962 %
Rwork0.207 104291 -
all0.209 --
obs-109736 99.799 %
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: 27.778 Å2
Baniso -1Baniso -2Baniso -3
1--0.456 Å20 Å20 Å2
2---0.456 Å20 Å2
3---0.911 Å2
Refinement stepCycle: LAST / Resolution: 2→84.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12158 0 148 704 13010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01312650
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711463
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.64717201
X-RAY DIFFRACTIONr_angle_other_deg1.2791.58126543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87151514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.58321.067703
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7151984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.05415105
X-RAY DIFFRACTIONr_chiral_restr0.0680.21555
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022849
X-RAY DIFFRACTIONr_nbd_refined0.1980.22562
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.210545
X-RAY DIFFRACTIONr_nbtor_refined0.1630.26082
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.25358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2693
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.245
X-RAY DIFFRACTIONr_nbd_other0.2230.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.21
X-RAY DIFFRACTIONr_mcbond_it1.9752.7786101
X-RAY DIFFRACTIONr_mcbond_other1.9752.7776100
X-RAY DIFFRACTIONr_mcangle_it3.124.1477600
X-RAY DIFFRACTIONr_mcangle_other3.124.1487601
X-RAY DIFFRACTIONr_scbond_it2.5923.1666548
X-RAY DIFFRACTIONr_scbond_other2.5923.1676549
X-RAY DIFFRACTIONr_scangle_it4.2094.6299586
X-RAY DIFFRACTIONr_scangle_other4.2094.639587
X-RAY DIFFRACTIONr_lrange_it6.02332.85814523
X-RAY DIFFRACTIONr_lrange_other5.99532.73814394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.323810.3127578X-RAY DIFFRACTION99.9247
2.052-2.1080.3363740.2997387X-RAY DIFFRACTION99.7045
2.108-2.1690.3053920.2657152X-RAY DIFFRACTION99.7092
2.169-2.2360.2993610.2566992X-RAY DIFFRACTION99.7423
2.236-2.3090.2993410.2416790X-RAY DIFFRACTION99.7064
2.309-2.390.2563400.2186637X-RAY DIFFRACTION99.7569
2.39-2.480.2923280.2246314X-RAY DIFFRACTION99.7148
2.48-2.5820.2763210.2096125X-RAY DIFFRACTION99.8606
2.582-2.6960.2523200.2075909X-RAY DIFFRACTION99.7917
2.696-2.8280.2863050.2115625X-RAY DIFFRACTION99.8653
2.828-2.9810.2342910.1965374X-RAY DIFFRACTION99.859
2.981-3.1610.2322780.1925096X-RAY DIFFRACTION99.8885
3.161-3.380.2562430.1984833X-RAY DIFFRACTION99.9016
3.38-3.650.252140.1914506X-RAY DIFFRACTION99.8519
3.65-3.9980.1892180.164178X-RAY DIFFRACTION99.9091
3.998-4.4690.1931970.1513815X-RAY DIFFRACTION99.8507
4.469-5.1590.1872140.1653340X-RAY DIFFRACTION99.8315
5.159-6.3150.2471280.2152936X-RAY DIFFRACTION99.7721
6.315-8.9150.2491190.1742314X-RAY DIFFRACTION99.8768

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