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- PDB-1nop: Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) i... -

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Basic information

Entry
Database: PDB / ID: 1nop
TitleCrystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide
Components
  • 5'-D(*AP*GP*AP*GP*TP*T)-3'
  • topoisomerase I-derived peptide
  • tyrosyl-DNA phosphodiesterase 1
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / vanadate complex / transition state mimic / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / DNA repair / intracellular membrane-bounded organelle ...3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / DNA repair / intracellular membrane-bounded organelle / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Tyrosyl-DNA phosphodiesterase I / Tyrosyl-DNA phosphodiesterase / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / : / DNA / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDavies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
Citation
Journal: Chem.Biol. / Year: 2003
Title: Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide
Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
#1: Journal: Structure / Year: 2002
Title: The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1
Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: Insights into substrate binding and catalytic mechanism of human tyrosyl-DNA phosphodiesterase (Tdp1) from vanadate- and tungstate-inhibited structures
Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 400COMPOUND THE STRUCTURE IS A MIMIC OF THE TRANSITION STATE FOR HYDROLYSIS OF THE TDP1 SUBSTRATE, A ...COMPOUND THE STRUCTURE IS A MIMIC OF THE TRANSITION STATE FOR HYDROLYSIS OF THE TDP1 SUBSTRATE, A COVALENT TOPOISOMERASE I-DNA COMPLEX.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*AP*GP*AP*GP*TP*T)-3'
F: 5'-D(*AP*GP*AP*GP*TP*T)-3'
A: tyrosyl-DNA phosphodiesterase 1
B: tyrosyl-DNA phosphodiesterase 1
C: topoisomerase I-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4097
Polymers114,1795
Non-polymers2302
Water1,72996
1
D: 5'-D(*AP*GP*AP*GP*TP*T)-3'
A: tyrosyl-DNA phosphodiesterase 1
C: topoisomerase I-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7154
Polymers57,6003
Non-polymers1151
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*AP*GP*AP*GP*TP*T)-3'
B: tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6943
Polymers56,5792
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.803, 104.719, 193.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsOne monomer of Tdp1 is the biologically active assembly

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Components

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


Mass: 1848.253 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence is derived from a sequence known to be a target for topoisomerase I
#2: Protein tyrosyl-DNA phosphodiesterase 1 / Tdp1


Mass: 54731.195 Da / Num. of mol.: 2 / Fragment: residues 149-608 / Mutation: D322N, M328T, F548L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 20127586, UniProt: Q9NUW8*PLUS
#3: Protein/peptide topoisomerase I-derived peptide


Mass: 1020.184 Da / Num. of mol.: 1 / Fragment: residues 720-727 / Source method: obtained synthetically
Details: This sequence occurs naturally in human topoisomerase I. This sequence includes the catalytic tyrosine residue that becomes transiently covalently attatched to the 3' end of DNA
#4: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: PEG 3000, sodium chloride, spermine, HEPES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 300011
2NaClSodium chloride11
3spermine11
4HEPES11
5PEG 300012
6NaClSodium chloride12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.5 mg/mlTdp11drop
23 mMsodium orthovanadate1drop
35 mM/lDNA1drop
420 mM/lpeptide1drop
522 %PEG33501reservoir
6100 mMHEPES1reservoirpH7.8
7200 mM1reservoirNaCl
810 mMspermine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→95.65 Å / Num. all: 43799 / Num. obs: 41018 / % possible obs: 93.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.085
Reflection shellResolution: 2.3→2.36 Å / Mean I/σ(I) obs: 2.08 / Rsym value: 0.339 / % possible all: 61.9
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 92.6 % / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 61.9 % / Rmerge(I) obs: 0.339

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→95.35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.144 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25185 2169 5 %RANDOM
Rwork0.20601 ---
all0.2083 43799 --
obs0.2083 41018 93.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.253 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å20 Å2
2--4.03 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6888 82 6 96 7072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217205
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9529805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485855
X-RAY DIFFRACTIONr_chiral_restr0.0960.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025436
X-RAY DIFFRACTIONr_nbd_refined0.2040.23047
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.345302
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.21
X-RAY DIFFRACTIONr_mcbond_it1.20524311
X-RAY DIFFRACTIONr_mcangle_it2.08936949
X-RAY DIFFRACTIONr_scbond_it1.17722894
X-RAY DIFFRACTIONr_scangle_it1.81932856
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 106 -
Rwork0.268 2019 -
obs--61.9 %
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 100 Å / Num. reflection obs: 38958 / Num. reflection Rfree: 2060 / % reflection Rfree: 5 % / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.387

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