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- PDB-7lpg: APE1 product complex with abasic ribonucleotide DNA -

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Basic information

Entry
Database: PDB / ID: 7lpg
TitleAPE1 product complex with abasic ribonucleotide DNA
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
  • DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsLYASE/DNA / DNA Repair / Abasic Ribonucleotide / AP-Endonuclease / LYASE / LYASE-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 / : / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / double-stranded telomeric DNA binding ...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 / : / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / double-stranded telomeric DNA binding / Displacement of DNA glycosylase by APEX1 / 3'-5'-DNA exonuclease activity / 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 / phosphodiesterase I 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 / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / regulation of mRNA stability / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / RNA-DNA hybrid ribonuclease activity / transcription corepressor activity / endonuclease activity / regulation of apoptotic process / DNA recombination / damaged DNA binding / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / nuclear speck / ribosome / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / 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: 2.08 Å
AuthorsFreudenthal, B.D. / Hoitsma, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES029203 United States
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Authors: Hoitsma, N.M. / Click, T.H. / Agarwal, P.K. / Freudenthal, B.D.
History
DepositionFeb 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA-(apurinic or apyrimidinic site) lyase
C: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
D: DNA-(apurinic or apyrimidinic site) lyase
E: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
A: DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)75,0495
Polymers75,0495
Non-polymers00
Water4,306239
1
B: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)31,1561
Polymers31,1561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12460 Å2
MethodPISA
2
C: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
D: DNA-(apurinic or apyrimidinic site) lyase
E: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
A: DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)43,8934
Polymers43,8934
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-24 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.118, 61.077, 73.039
Angle α, β, γ (deg.)83.682, 78.066, 87.491
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein DNA-(apurinic or apyrimidinic site) lyase / APEX1 / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / APE-1 / REF-1 / Redox factor-1


Mass: 31156.477 Da / Num. of mol.: 2 / Mutation: C138A
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
#2: DNA chain DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 6449.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')


Mass: 3226.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.08→25 Å / Num. obs: 75243 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.64 Å2 / Rrim(I) all: 0.119 / Net I/σ(I): 12.5
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 3.3 % / Num. unique obs: 2151 / CC1/2: 0.68 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFF

5dff


Resolution: 2.08→23.69 Å / SU ML: 0.3053 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.0759
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2627 3446 4.58 %
Rwork0.2194 71797 -
obs0.2214 75243 84.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.64 Å2
Refinement stepCycle: LAST / Resolution: 2.08→23.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 848 0 239 5403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00895385
X-RAY DIFFRACTIONf_angle_d1.10987479
X-RAY DIFFRACTIONf_chiral_restr0.0607803
X-RAY DIFFRACTIONf_plane_restr0.0062821
X-RAY DIFFRACTIONf_dihedral_angle_d27.22172070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.110.3424910.3371929X-RAY DIFFRACTION55.83
2.11-2.140.36181310.31622682X-RAY DIFFRACTION81.25
2.14-2.170.31371350.30772818X-RAY DIFFRACTION82.12
2.17-2.20.3681470.29672854X-RAY DIFFRACTION82.13
2.2-2.240.35921260.30342738X-RAY DIFFRACTION82.73
2.24-2.280.32061430.28062867X-RAY DIFFRACTION83.56
2.28-2.320.28651400.27962884X-RAY DIFFRACTION84.71
2.32-2.360.32631280.28252842X-RAY DIFFRACTION84.23
2.36-2.410.3811340.29132906X-RAY DIFFRACTION85.88
2.41-2.460.36491320.28772938X-RAY DIFFRACTION85.28
2.46-2.520.32531410.28362937X-RAY DIFFRACTION86.07
2.52-2.580.3191380.27922899X-RAY DIFFRACTION85.5
2.58-2.650.30661480.27772934X-RAY DIFFRACTION85.9
2.65-2.730.37341440.28212983X-RAY DIFFRACTION87.2
2.73-2.820.40181420.27962845X-RAY DIFFRACTION85.59
2.82-2.920.32871460.28623031X-RAY DIFFRACTION86.28
2.92-3.040.35851370.2972885X-RAY DIFFRACTION86
3.04-3.180.40821450.27422957X-RAY DIFFRACTION87.18
3.18-3.340.24811430.22023020X-RAY DIFFRACTION88.15
3.34-3.550.2281480.19692955X-RAY DIFFRACTION88.71
3.55-3.820.20061480.18323057X-RAY DIFFRACTION89.08
3.82-4.210.2131450.1862932X-RAY DIFFRACTION86.58
4.21-4.810.19061420.15673014X-RAY DIFFRACTION87.47
4.81-6.040.24771410.16782968X-RAY DIFFRACTION87.68
6.05-23.690.16611310.16242922X-RAY DIFFRACTION85.37

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