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- PDB-8xwu: Crystal structure of human 8-oxoguanine glycosylase K249H mutant ... -

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Basic information

Entry
Database: PDB / ID: 8xwu
TitleCrystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction intermediate derived from the crystal soaked into the solution at pH 4.0 under 277 K for 24 hourss
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*TP*AP*CP*C)-3')
  • N-glycosylase/DNA lyase
KeywordsDNA/HYDROLASE / DNA / repair / LYASE / DNA-HYDROLASE complex
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 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / 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 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / 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 / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cellular response to reactive oxygen species / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / response to oxidative stress / endonuclease activity / microtubule binding / damaged DNA binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrial matrix / 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 / 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
: / DNA / DNA (> 10) / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsUnno, M. / Koga, M. / Minowa, N. / Komuro, S. / Tanaka, Y.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K05320 Japan
Japan Society for the Promotion of Science (JSPS)19K05705 Japan
Japan Society for the Promotion of Science (JSPS)19K06507 Japan
Japan Society for the Promotion of Science (JSPS)16K07261 Japan
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Capturing a glycosylase reaction intermediate in DNA repair by freeze-trapping of a pH-responsive hOGG1 mutant.
Authors: Unno, M. / Morikawa, M. / Sychrovsky, V. / Koga, M. / Minowa, N. / Komuro, S. / Shimizu, M. / Fukuta, M. / Tsuyuguchi, F. / Mano, H. / Ochi, Y. / Nakashima, K. / Okamoto, Y. / Saio, T. / Hattori, Y. / Tanaka, Y.
History
DepositionJan 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*A)-3')
D: DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
A: N-glycosylase/DNA lyase
B: DNA (5'-D(P*GP*TP*CP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,52710
Polymers46,8214
Non-polymers7066
Water6,810378
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.873, 69.404, 88.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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DNA chain , 3 types, 3 molecules CDB

#1: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*A)-3')


Mass: 2411.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')


Mass: 4635.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*TP*AP*CP*C)-3')


Mass: 2073.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein , 1 types, 1 molecules A

#3: Protein N-glycosylase/DNA lyase


Mass: 37700.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGG1, MMH, MUTM, OGH1 / Production host: Escherichia coli (E. coli)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase

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Non-polymers , 4 types, 384 molecules

#5: Chemical ChemComp-A1LXK / [(2~{R},3~{S},5~{S})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-2,3,5-tris(oxidanyl)pentyl] dihydrogen phosphate


Mass: 381.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O9P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: sodium cacodylate, PEG 4000, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.04 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.68→46.18 Å / Num. obs: 44239 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.83 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.3
Reflection shellResolution: 1.68→1.71 Å / Num. unique obs: 2215 / CC1/2: 0.514

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→46.18 Å / SU ML: 0.1925 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1055
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2135 2160 4.89 %
Rwork0.1689 42003 -
obs0.1711 44163 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.03 Å2
Refinement stepCycle: LAST / Resolution: 1.68→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 471 184 378 3524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01523392
X-RAY DIFFRACTIONf_angle_d1.6564756
X-RAY DIFFRACTIONf_chiral_restr0.0647510
X-RAY DIFFRACTIONf_plane_restr0.0121514
X-RAY DIFFRACTIONf_dihedral_angle_d23.0316687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.32161440.28862705X-RAY DIFFRACTION98.07
1.72-1.760.28541470.24912765X-RAY DIFFRACTION99.62
1.76-1.810.25231470.22142767X-RAY DIFFRACTION99.93
1.81-1.860.25691350.19492762X-RAY DIFFRACTION99.97
1.86-1.920.23841530.19692764X-RAY DIFFRACTION100
1.92-1.990.24711840.18452707X-RAY DIFFRACTION99.97
1.99-2.070.25181340.17122808X-RAY DIFFRACTION99.97
2.07-2.170.22631250.16392806X-RAY DIFFRACTION100
2.17-2.280.22561380.1672766X-RAY DIFFRACTION99.97
2.28-2.420.22861480.17092795X-RAY DIFFRACTION99.93
2.42-2.610.21841390.16892823X-RAY DIFFRACTION100
2.61-2.870.20931150.17362827X-RAY DIFFRACTION99.97
2.87-3.290.19191500.16182855X-RAY DIFFRACTION100
3.29-4.140.16471380.13632866X-RAY DIFFRACTION100
4.14-46.180.19181630.15152987X-RAY DIFFRACTION99.9

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