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- PDB-7lph: APE1 Mn-bound product complex with abasic ribonucleotide DNA -

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Basic information

Entry
Database: PDB / ID: 7lph
TitleAPE1 Mn-bound 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 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 / regulation of mRNA stability / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / 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: 1.99 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1046
Polymers75,0495
Non-polymers551
Water5,855325
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 area12550 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9485
Polymers43,8934
Non-polymers551
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-35 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.249, 61.570, 72.964
Angle α, β, γ (deg.)83.652, 78.147, 87.418
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules BD

#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

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DNA chain , 3 types, 3 molecules CEA

#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)

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Non-polymers , 2 types, 326 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
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: Aug 27, 2020
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: 66383 / % possible obs: 96.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 23.7 Å2 / Rrim(I) all: 0.08 / Net I/σ(I): 21.7
Reflection shellResolution: 1.99→2.03 Å / Redundancy: 3.3 % / Num. unique obs: 2235 / CC1/2: 0.789 / Rrim(I) all: 0.574 / % possible all: 88.5

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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: 1.99→24.72 Å / SU ML: 0.2383 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.9978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 2798 4.21 %
Rwork0.1919 63585 -
obs0.1938 66383 65.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.67 Å2
Refinement stepCycle: LAST / Resolution: 1.99→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4314 848 1 325 5488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00975476
X-RAY DIFFRACTIONf_angle_d1.26367617
X-RAY DIFFRACTIONf_chiral_restr0.0734814
X-RAY DIFFRACTIONf_plane_restr0.0064825
X-RAY DIFFRACTIONf_dihedral_angle_d27.0782127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.030.3198610.2731398X-RAY DIFFRACTION28.56
2.03-2.070.3153770.24691734X-RAY DIFFRACTION35.68
2.07-2.10.2588870.25791993X-RAY DIFFRACTION40.55
2.1-2.150.3372930.24362126X-RAY DIFFRACTION43.87
2.15-2.190.2984980.24562223X-RAY DIFFRACTION45.47
2.19-2.250.28421010.25772307X-RAY DIFFRACTION46.76
2.25-2.30.27941020.25322288X-RAY DIFFRACTION47.35
2.3-2.360.25451080.24852422X-RAY DIFFRACTION49.76
2.36-2.430.29771170.24042657X-RAY DIFFRACTION53.35
2.43-2.510.32921190.23422781X-RAY DIFFRACTION57.24
2.51-2.60.23851340.22633098X-RAY DIFFRACTION63.15
2.6-2.710.28021520.23133420X-RAY DIFFRACTION69.93
2.71-2.830.23151620.22383683X-RAY DIFFRACTION76.38
2.83-2.980.2751830.23484087X-RAY DIFFRACTION82.88
2.98-3.160.28731910.2184359X-RAY DIFFRACTION88.62
3.16-3.410.22231960.19264494X-RAY DIFFRACTION91.57
3.41-3.750.231970.17294486X-RAY DIFFRACTION93.21
3.75-4.290.19852030.14964626X-RAY DIFFRACTION93.73
4.29-5.390.18562110.14484656X-RAY DIFFRACTION95.81
5.39-24.720.20412060.15744747X-RAY DIFFRACTION96.85

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