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- PDB-6w4t: APE1 Y269A phosphorothioate substrate complex with abasic DNA -

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Basic information

Entry
Database: PDB / ID: 6w4t
TitleAPE1 Y269A phosphorothioate substrate complex with abasic DNA
Components
  • DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsLYASE/DNA / DNA Repair / AP-Endonuclease / DNA Binding / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / 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 telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III ...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 telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / 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 / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / chromatin DNA binding / base-excision repair / 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. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase ...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. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
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: 2.77 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: Nucleic Acids Res. / Year: 2020
Title: AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.
Authors: Hoitsma, N.M. / Whitaker, A.M. / Beckwitt, E.C. / Jang, S. / Agarwal, P.K. / Van Houten, B. / Freudenthal, B.D.
History
DepositionMar 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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
A: DNA-(apurinic or apyrimidinic site) lyase
P: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
V: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
B: DNA-(apurinic or apyrimidinic site) lyase
C: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)87,7216
Polymers87,7216
Non-polymers00
Water70339
1
A: DNA-(apurinic or apyrimidinic site) lyase
P: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
V: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)43,8613
Polymers43,8613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-21 kcal/mol
Surface area17480 Å2
MethodPISA
2
B: DNA-(apurinic or apyrimidinic site) lyase
C: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)43,8613
Polymers43,8613
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-18 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.659, 148.315, 153.235
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

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


Mass: 31064.379 Da / Num. of mol.: 2 / Mutation: Y269A, 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(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')


Mass: 6347.127 Da / Num. of mol.: 2 / 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*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 6449.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 27% PEG 3350, 100 mM Bis Tris Propane (pH 6.5), 200 mM Sodium Fluoride

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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: Nov 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→48.29 Å / Num. obs: 27446 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 56.88 Å2 / Rrim(I) all: 0.261 / Net I/σ(I): 7.4
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 6.8 % / Num. unique obs: 3910 / CC1/2: 0.395 / Rrim(I) all: 2.67 / % possible all: 100

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.17.1_3660refinement
Blu-Icedata collection
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFF

5dff


Resolution: 2.77→48.29 Å / SU ML: 0.5252 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.4919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2741 1267 4.69 %
Rwork0.2214 25759 -
obs0.224 27026 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.9 Å2
Refinement stepCycle: LAST / Resolution: 2.77→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 1691 0 39 6110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01756407
X-RAY DIFFRACTIONf_angle_d1.43169025
X-RAY DIFFRACTIONf_chiral_restr0.0891976
X-RAY DIFFRACTIONf_plane_restr0.0082874
X-RAY DIFFRACTIONf_dihedral_angle_d28.85912478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.880.44781390.39172560X-RAY DIFFRACTION90.39
2.88-3.010.43461260.34142832X-RAY DIFFRACTION99.13
3.01-3.170.34461360.27542837X-RAY DIFFRACTION99.83
3.17-3.370.26231270.24282871X-RAY DIFFRACTION99.6
3.37-3.630.34491520.23982855X-RAY DIFFRACTION99.73
3.63-40.27621400.21632874X-RAY DIFFRACTION99.97
4-4.570.24271650.19112894X-RAY DIFFRACTION99.74
4.57-5.760.24811320.1912957X-RAY DIFFRACTION99.84
5.76-48.290.20961500.18183079X-RAY DIFFRACTION99.75

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