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- PDB-1de9: HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION -

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Basic information

Entry
Database: PDB / ID: 1de9
TitleHUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION
Components
  • 5'-d(*CP*TP*AP*C)-3'
  • 5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'
  • 5'-d(P*(3DR)P*GP*AP*TP*C)-3'
  • MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
KeywordsLYASE/DNA / ENZYME:DNA COMPLEX / DNA REPAIR ABASIC SITE / AP ENDONUCLEASE / LYASE-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 / endonuclease activity / DNA recombination / chromosome, telomeric region / damaged DNA binding / oxidoreductase activity / transcription coactivator 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. / 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 repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsMol, C.D. / Izumi, T. / Mitra, S. / Tainer, J.A.
CitationJournal: Nature / Year: 2000
Title: DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination
Authors: Mol, C.D. / Izumi, T. / Mitra, S. / Tainer, J.A.
History
DepositionNov 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 5'-d(*CP*TP*AP*C)-3'
Y: 5'-d(P*(3DR)P*GP*AP*TP*C)-3'
Z: 5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'
U: 5'-d(*CP*TP*AP*C)-3'
V: 5'-d(P*(3DR)P*GP*AP*TP*C)-3'
W: 5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'
A: MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
B: MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,14210
Polymers73,0328
Non-polymers1102
Water00
1
X: 5'-d(*CP*TP*AP*C)-3'
Y: 5'-d(P*(3DR)P*GP*AP*TP*C)-3'
Z: 5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'
A: MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5715
Polymers36,5164
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
U: 5'-d(*CP*TP*AP*C)-3'
V: 5'-d(P*(3DR)P*GP*AP*TP*C)-3'
W: 5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'
B: MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5715
Polymers36,5164
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.06, 98.35, 101.05
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 1150.806 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-d(P*(3DR)P*GP*AP*TP*C)-3'


Mass: 1370.926 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'


Mass: 2795.846 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Protein MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE / E.C.4.2.99.18 / APE1


Mass: 31198.559 Da / Num. of mol.: 2 / Fragment: APE1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn

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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: 3.04 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPEG 2000, LITHIUM SULFATE, MANGANESE CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1LI2SO411
2MNCL211
3MPEG 200011
4MPEG 200012
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mM1dropMnCl2
220 %mPEG50001reservoir
350 mMMES1reservoir
4200 mM1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 17008 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.45 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.424 / % possible all: 92.4
Reflection shell
*PLUS
% possible obs: 92.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementResolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
Details: THE EXACT CONFORMATION AND BASE-PAIRING OF THE DNA IS STRINGLY AN ARTIFACT OF THE CRYSTAL PACKING. THE DNA PHOSPHODIESTER BACKBONE CLOSELY RESEMBLES THAT OF THE UNCLEAVED COMPLEX, 1DE8
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1376 10 %RANDOM
Rwork0.183 ---
obs0.1831 12390 --
all-13766 --
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 712 2 0 5088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1.354
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.354
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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