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- PDB-1lpq: Human DNA Topoisomerase I (70 Kda) In Non-Covalent Complex With A... -

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Entry
Database: PDB / ID: 1lpq
TitleHuman DNA Topoisomerase I (70 Kda) In Non-Covalent Complex With A 22 Base Pair DNA Duplex Containing an 8-oxoG Lesion
Components
  • 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*(8OG)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
  • 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'
  • DNA topoisomerase ITopoisomerase
KeywordsISOMERASE/DNA / protein-DNA complex / DNA damage / induced conformational change / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / programmed cell death / embryonic cleavage / supercoiled DNA binding / DNA binding, bending / SUMOylation of DNA replication proteins / DNA topological change / male germ cell nucleus / chromosome segregation ...DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / programmed cell death / embryonic cleavage / supercoiled DNA binding / DNA binding, bending / SUMOylation of DNA replication proteins / DNA topological change / male germ cell nucleus / chromosome segregation / P-body / protein-DNA complex / circadian regulation of gene expression / fibrillar center / circadian rhythm / single-stranded DNA binding / chromosome / perikaryon / double-stranded DNA binding / peptidyl-serine phosphorylation / DNA replication / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / phosphorylation / protein serine/threonine kinase activity / chromatin binding / nucleolus / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Topoisomerase I; Chain A, domain 4 - #10 / : / Yeast DNA topoisomerase - domain 1 / DNA Topoisomerase I; domain 2 / DNA Topoisomerase I, domain 2 / DNA topoisomerase I, DNA binding, eukaryotic-type / DNA topoisomerase I, DNA binding, N-terminal domain 2 / DNA topoisomerase I, DNA binding, N-terminal domain 1 / DNA topoisomerase I, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha/beta subdomain ...Topoisomerase I; Chain A, domain 4 - #10 / : / Yeast DNA topoisomerase - domain 1 / DNA Topoisomerase I; domain 2 / DNA Topoisomerase I, domain 2 / DNA topoisomerase I, DNA binding, eukaryotic-type / DNA topoisomerase I, DNA binding, N-terminal domain 2 / DNA topoisomerase I, DNA binding, N-terminal domain 1 / DNA topoisomerase I, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha/beta subdomain / Topoisomerase I C-terminal domain / DNA topoisomerase I, DNA binding, eukaryotic-type, N-terminal domain superfamily / Eukaryotic DNA topoisomerase I, DNA binding fragment / C-terminal topoisomerase domain / DNA Topoisomerase I (eukaryota) / Topoisomerase (Topo) IB-type catalytic domain profile. / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type / Eukaryotic DNA topoisomerase I, catalytic core / DNA breaking-rejoining enzyme, catalytic core / Topoisomerase I; Chain A, domain 4 / Beta Complex / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsLesher, D.T. / Pommier, Y. / Stewart, L. / Redinbo, M.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: 8-Oxoguanine rearranges the active site of human topoisomerase I
Authors: Lesher, D.T. / Pommier, Y. / Stewart, L. / Redinbo, M.R.
History
DepositionMay 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*(8OG)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
C: 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'
A: DNA topoisomerase I


Theoretical massNumber of molelcules
Total (without water)80,2803
Polymers80,2803
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.200, 122.500, 72.000
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*(8OG)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'


Mass: 6822.467 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'


Mass: 6690.362 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA topoisomerase I / Topoisomerase


Mass: 66767.062 Da / Num. of mol.: 1 / Mutation: Y723F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, DNA topoisomerase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Tris-HCl, MES, PEG 400, Magnesium chloride, dithiothreitol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HClTris11
2MES11
3PEG 40011
4MgCl211
5dithiothreitol11
6MgCl212
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / Details: Stewart, L., (1998) Science, 279, 1534.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mM1droppH6.0
28.6 mMMES-HCl1droppH6.8
312 %(v/v)PEG4001drop
462 mM1dropMgCl2
514 mM1drop
60.01 mMoligonucleotide1drop
70.9 mM1dropNaCl
81.4 mg/mlprotein1drop
9water1drop0.002ml
100.3 mMEDTA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1
DetectorType: BRANDEIS / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.14→20 Å / Num. obs: 17165 / % possible obs: 95.6 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 2.5 % / Rmerge(I) obs: 0.334 / Rsym value: 0.2 / Net I/σ(I): 11.9
Reflection shellResolution: 3.14→3.19 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.265 / % possible all: 90.5
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 2.22 % / Num. measured all: 38120 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 90.5 % / Rmerge(I) obs: 0.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→19.87 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 1588348.29 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1132 6.9 %RANDOM
Rwork0.256 ---
obs-16401 95.5 %-
Displacement parametersBiso mean: 64.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.68 Å20 Å213.32 Å2
2--8.89 Å20 Å2
3----4.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.14→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4457 897 0 27 5381
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it10.62
X-RAY DIFFRACTIONc_scangle_it12.712.5
LS refinement shellResolution: 3.14→3.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 184 7.2 %
Rwork0.36 2380 -
obs--90.1 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00821
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
LS refinement shell
*PLUS
Rfactor Rfree: 0.391 / Rfactor Rwork: 0.36

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