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- PDB-9dp1: APE1 N174A Substrate Complex with Abasic DNA -

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Basic information

Entry
Database: PDB / ID: 9dp1
TitleAPE1 N174A Substrate Complex with Abasic DNA
Components
  • DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
  • DNA repair nuclease/redox regulator APEX1, mitochondrial
KeywordsHYDROLASE/DNA / APE1 / APEX1 / Endonuclease / DNA Repair / HYDROLASE-DNA complex
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / exodeoxyribonuclease III / phosphodiesterase I activity ...Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / exodeoxyribonuclease III / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 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 / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / endonuclease activity / regulation of apoptotic process / DNA recombination / damaged DNA binding / chromosome, telomeric region / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsDeHart, K.M. / Freudenthal, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES029203 United States
CitationJournal: To Be Published
Title: N174 Physically and Chemically Stabilizes the Endonuclease Reaction of APE1
Authors: DeHart, K.D. / Hoitsma, N.M. / Thompson, S.H. / Freudenthal, B.D.
History
DepositionSep 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair nuclease/redox regulator APEX1, mitochondrial
B: DNA repair nuclease/redox regulator APEX1, mitochondrial
D: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
E: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)75,0084
Polymers75,0084
Non-polymers00
Water4,882271
1
A: DNA repair nuclease/redox regulator APEX1, mitochondrial
D: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
E: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)43,8953
Polymers43,8953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-18 kcal/mol
Surface area17130 Å2
MethodPISA
2
B: DNA repair nuclease/redox regulator APEX1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)31,1131
Polymers31,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.943, 60.498, 73.075
Angle α, β, γ (deg.)81.81, 75.60, 88.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA repair nuclease/redox regulator APEX1, mitochondrial


Mass: 31113.453 Da / Num. of mol.: 2 / Mutation: tr1-42, C138A, N174A
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
#2: DNA chain DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')


Mass: 6316.050 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*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 6465.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium citrate, pH 5.0, 200 mM magnesium chloride, 16-21% PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 8, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→25.06 Å / Num. obs: 29791 / % possible obs: 96.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 30.56 Å2 / Rrim(I) all: 0.133 / Net I/σ(I): 7.6
Reflection shellResolution: 2.29→2.34 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.39 / Num. unique obs: 1460 / CC1/2: 0.915 / Rrim(I) all: 0.215 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Blu-Icedata collection
XDSdata reduction
HKL-3000705cdata scaling
PHENIX1.19.2-4158-000phasing
Coot0.9model building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→25.06 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 2003 6.72 %
Rwork0.2298 --
obs0.2312 29791 91.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→25.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4156 850 0 271 5277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125215
X-RAY DIFFRACTIONf_angle_d1.7057256
X-RAY DIFFRACTIONf_dihedral_angle_d22.3541972
X-RAY DIFFRACTIONf_chiral_restr0.104789
X-RAY DIFFRACTIONf_plane_restr0.007788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.3486800.28771171X-RAY DIFFRACTION54
2.35-2.410.29691570.26772078X-RAY DIFFRACTION96
2.41-2.480.31941540.2682059X-RAY DIFFRACTION96
2.48-2.560.32131500.26392110X-RAY DIFFRACTION97
2.56-2.650.32861490.28152033X-RAY DIFFRACTION95
2.65-2.760.29351570.26762127X-RAY DIFFRACTION96
2.76-2.890.28051370.25732066X-RAY DIFFRACTION97
2.89-3.040.28821550.24652102X-RAY DIFFRACTION98
3.04-3.230.24591470.22572099X-RAY DIFFRACTION97
3.23-3.480.2171500.22032056X-RAY DIFFRACTION95
3.48-3.830.25651490.2232002X-RAY DIFFRACTION94
3.83-4.380.2161460.20212061X-RAY DIFFRACTION94
4.38-5.50.2041430.19372050X-RAY DIFFRACTION95
5.5-25.060.20421290.2181774X-RAY DIFFRACTION83

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