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- PDB-9kky: Co-crystal structure of human 8-oxoguanine glycosylase N149C muta... -

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Basic information

Entry
Database: PDB / ID: 9kky
TitleCo-crystal structure of human 8-oxoguanine glycosylase N149C mutant with DNA containing photocaged 8-oxoguanine
Components
  • DNA (5'-D(*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*G)-3')
  • N-glycosylase/DNA lyase
KeywordsLYASE / DNA-glycosylase / DNA repair / base excision repair / hOGG1 / photocaged / O6-(o-nitrophenisopropyl) 8-oxoguanine
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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / 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 / endonuclease activity / microtubule binding / response to oxidative stress / damaged DNA binding / nuclear speck / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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: 2.81 Å
AuthorsImura, T. / Yang, K.-C. / Hosokawa, Y. / Shih, H.-Y. / Ban, Y. / Yamamoto, J. / Maestre-Reyna, M.
Funding support Taiwan, Japan, 2items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)NSTC, 111-2113-M-002-029-MY3 Taiwan
Japan Science and TechnologyJPMJFR2057 Japan
CitationJournal: Iucrj / Year: 2025
Title: Revisiting the co-crystal structure of a DNA glycosylase with photocaged substrate: a suitable time-resolved crystallography target?
Authors: Imura, T. / Hosokawa, Y. / Yang, K.C. / Ban, Y. / Shih, H.Y. / Yamamoto, J. / Maestre-Reyna, M.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*G)-3')
C: DNA (5'-D(*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3')
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9788
Polymers47,7253
Non-polymers2525
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-57 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.673, 89.673, 211.766
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

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DNA chain , 2 types, 2 molecules BC

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


Mass: 4939.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*AP*(8OG)P*GP*TP*CP*TP*AP*C)-3')


Mass: 4875.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 1 types, 1 molecules A

#3: Protein N-glycosylase/DNA lyase


Mass: 37910.922 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 BL21(DE3) (bacteria)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase

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Non-polymers , 3 types, 54 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.58 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, calcium chloride, sodium cacodylate / PH range: 6-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 14869 / % possible obs: 96.4 % / Redundancy: 4.5267 % / Biso Wilson estimate: 69.03 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.92
Reflection shellResolution: 2.65→2.81 Å / Redundancy: 4.866 % / Mean I/σ(I) obs: 1.83 / Num. unique obs: 2389 / CC1/2: 0.522 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMAC5.8.0415refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQR

1yqr


Resolution: 2.81→29.35 Å / SU ML: 0.3393 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2623 920 7.22 %
Rwork0.224 11814 -
obs0.2268 12734 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.19 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 372 10 54 2817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842888
X-RAY DIFFRACTIONf_angle_d1.2424021
X-RAY DIFFRACTIONf_chiral_restr0.0883446
X-RAY DIFFRACTIONf_plane_restr0.0094456
X-RAY DIFFRACTIONf_dihedral_angle_d20.58341039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.960.38131220.31581656X-RAY DIFFRACTION99.66
2.96-3.140.40121290.31211649X-RAY DIFFRACTION99.05
3.14-3.390.31491300.27311669X-RAY DIFFRACTION99.01
3.39-3.720.24541150.22911678X-RAY DIFFRACTION98.35
3.73-4.260.24511440.19151651X-RAY DIFFRACTION97.29
4.26-5.370.22451490.19171692X-RAY DIFFRACTION98.19
5.37-29.350.24681310.21751819X-RAY DIFFRACTION96.58
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.33773386742-2.660160558330.02946934133112.106178471090.2844081672928.18096234118-1.47115002785-0.03034404251152.21802691833-0.09235123196170.1675360922881.06329325885-1.79321297879-1.490981567521.2661596851.810368490210.282620226809-0.4390460116311.62295480697-0.2729263341321.76168769098-19.393999146633.648870451713.3037536231
25.82787382575-4.627675476334.964229556344.34842951148-3.638572947674.36286749590.0740360342682-0.6715755595121.232180665690.466447427798-0.4199797133911.18650194827-2.717952518370.4519594342150.4572941000621.46296776614-0.02190187558370.02996896228351.41573461921-0.08841019270461.15705738636-20.588792461529.59886423339.83930921809
32.449524819430.077884200156-0.1602954222330.367818450601-0.4674135852252.33253734616-0.0688558666621-0.07936741332810.270287463836-0.111202136489-0.0519294262903-0.00775687605984-0.1658687916970.1109387151670.1197282236470.804454825944-0.00367395496238-0.07437207091620.578189620075-0.01861703792620.300847095462-2.0192158038722.1610271897-3.28452602989
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 11 )BA1 - 11
22chain 'C' and (resid 22 through 29 )CB22 - 29
33chain 'A' and (resid 11 through 329 )AC - E11 - 3291

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