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- PDB-7suv: APE1 exonuclease substrate complex with 8oxoG opposite A -

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Basic information

Entry
Database: PDB / ID: 7suv
TitleAPE1 exonuclease substrate complex with 8oxoG opposite A
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
  • DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsHYDROLASE/DNA / nuclease / DNA Repair protein / DNA binding protein / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity ...Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 3'-5'-DNA exonuclease activity / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / regulation of apoptotic process / DNA recombination / endonuclease activity / chromosome, telomeric region / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / ribosome / nuclear speck / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWhitaker, A.W. / Freudenthal, B.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)K99-ES031148 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01-ES029203 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM128562 United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Processing oxidatively damaged bases at DNA strand breaks by APE1.
Authors: Whitaker, A.M. / Stark, W.J. / Freudenthal, B.D.
History
DepositionNov 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: 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
C: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
D: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
E: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
A: DNA-(apurinic or apyrimidinic site) lyase
B: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)75,1935
Polymers75,1935
Non-polymers00
Water4,738263
1
C: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
D: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
E: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
B: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)44,0394
Polymers44,0394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-20 kcal/mol
Surface area17770 Å2
MethodPISA
2
A: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)31,1551
Polymers31,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.112, 66.486, 91.983
Angle α, β, γ (deg.)90.000, 110.693, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')


Mass: 3117.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 6433.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein DNA-(apurinic or apyrimidinic site) lyase / APEX1 / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / APE-1 / REF-1 / Redox factor-1


Mass: 31154.504 Da / Num. of mol.: 2 / Mutation: E96Q, C138A, D210N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APEX1, APE, APE1, APEX, APX, HAP1, REF1 / Production host: Escherichia coli (E. coli)
References: UniProt: P27695, Hydrolases; Acting on ester bonds, DNA-(apurinic or apyrimidinic site) lyase
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.99→25 Å / Num. obs: 96631 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 35.7 Å2 / Rpim(I) all: 0.063 / Rrim(I) all: 0.145 / Net I/σ(I): 15.04
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.71 / Num. unique obs: 189625 / CC1/2: 0.829 / Rpim(I) all: 0.404 / Rrim(I) all: 0.674 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158phasing
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFI

5dfi


Resolution: 1.99→24.96 Å / SU ML: 0.2967 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.0064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2649 3527 3.66 %
Rwork0.226 92752 -
obs0.2274 96279 89.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.81 Å2
Refinement stepCycle: LAST / Resolution: 1.99→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 859 0 263 5512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085516
X-RAY DIFFRACTIONf_angle_d1.01127669
X-RAY DIFFRACTIONf_chiral_restr0.055817
X-RAY DIFFRACTIONf_plane_restr0.0098849
X-RAY DIFFRACTIONf_dihedral_angle_d22.30562113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.3921920.34682464X-RAY DIFFRACTION59.32
2.02-2.050.40691380.32913591X-RAY DIFFRACTION87.35
2.05-2.080.4251430.33943628X-RAY DIFFRACTION86.69
2.08-2.110.33241460.31473731X-RAY DIFFRACTION90.2
2.11-2.140.3531430.29573927X-RAY DIFFRACTION92
2.14-2.180.33911590.2923773X-RAY DIFFRACTION92.52
2.18-2.220.32151440.2923863X-RAY DIFFRACTION92.07
2.22-2.260.34921350.32343759X-RAY DIFFRACTION90.96
2.26-2.310.45361270.35083411X-RAY DIFFRACTION80.56
2.31-2.360.35441480.32323778X-RAY DIFFRACTION91.28
2.36-2.410.39061560.31383844X-RAY DIFFRACTION92.46
2.41-2.470.37951350.30053730X-RAY DIFFRACTION90.75
2.47-2.540.36031320.31723419X-RAY DIFFRACTION80.85
2.54-2.620.3941290.30873766X-RAY DIFFRACTION90.62
2.62-2.70.29041410.293791X-RAY DIFFRACTION90.93
2.7-2.80.32271460.2823666X-RAY DIFFRACTION88
2.8-2.910.34511440.28663708X-RAY DIFFRACTION89.54
2.91-3.040.30081450.27813646X-RAY DIFFRACTION87.29
3.04-3.20.25831440.25183686X-RAY DIFFRACTION88.23
3.2-3.40.2021350.22793651X-RAY DIFFRACTION87.99
3.4-3.660.21121420.19993908X-RAY DIFFRACTION93.58
3.66-4.030.2921490.18473842X-RAY DIFFRACTION92.71
4.03-4.610.19321470.15333918X-RAY DIFFRACTION93.84
4.61-5.790.19441490.16154097X-RAY DIFFRACTION98.33
5.79-24.960.19861580.15974155X-RAY DIFFRACTION99.47

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