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- PDB-5j3p: Crystal structure of the catalytic domain of human tyrosyl DNA ph... -

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Basic information

Entry
Database: PDB / ID: 5j3p
TitleCrystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2
ComponentsTyrosyl-DNA phosphodiesterase 2
KeywordsHYDROLASE / tyrosyl / DNA phosphodiesterase 2 / catalytic domain
Function / homology
Function and homology information


tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / aggresome / neuron development / Nonhomologous End-Joining (NHEJ) / PML body / transcription corepressor activity / double-strand break repair ...tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / aggresome / neuron development / Nonhomologous End-Joining (NHEJ) / PML body / transcription corepressor activity / double-strand break repair / single-stranded DNA binding / manganese ion binding / cell surface receptor signaling pathway / nuclear body / nucleolus / magnesium ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
UBA-like domain / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / UBA-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHornyak, P. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
Cancer Research UKC6563/A16771 United Kingdom
Cancer Research UKC480/A11411 United Kingdom
CitationJournal: Biochem.J. / Year: 2016
Title: Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
Authors: Hornyak, P. / Askwith, T. / Walker, S. / Komulainen, E. / Paradowski, M. / Pennicott, L.E. / Bartlett, E.J. / Brissett, N.C. / Raoof, A. / Watson, M. / Jordan, A.M. / Ogilvie, D.J. / Ward, S. ...Authors: Hornyak, P. / Askwith, T. / Walker, S. / Komulainen, E. / Paradowski, M. / Pennicott, L.E. / Bartlett, E.J. / Brissett, N.C. / Raoof, A. / Watson, M. / Jordan, A.M. / Ogilvie, D.J. / Ward, S.E. / Atack, J.R. / Pearl, L.H. / Caldecott, K.W. / Oliver, A.W.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-DNA phosphodiesterase 2
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7895
Polymers57,6492
Non-polymers1413
Water1086
1
A: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8492
Polymers28,8241
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9413
Polymers28,8241
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.545, 92.545, 119.075
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Tyrosyl-DNA phosphodiesterase 2 / hTDP2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ETS1-associated protein 2 ...hTDP2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ETS1-associated protein 2 / ETS1-associated protein II / EAPII / TRAF and TNF receptor-associated protein / Tyrosyl-RNA phosphodiesterase / VPg unlinkase


Mass: 28824.314 Da / Num. of mol.: 2 / Mutation: C273Ser
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDP2, EAP2, TTRAP, AD-022 / Production host: Escherichia coli (E. coli) / Strain (production host): B832(DE3)
References: UniProt: O95551, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris propane pH 7.0, 0.5 M NaCl, 0.05 M magnesium acetate, 1.5% v/v Trimethylamine N-oxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→47.793 Å / Num. obs: 20418 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC1/2: 1 / Rmerge(I) obs: 0.151 / Net I/σ(I): 9.6
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 1.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GYZ

4gyz


Resolution: 3.1→47.793 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 35.55
RfactorNum. reflection% reflection
Rfree0.2914 970 4.75 %
Rwork0.2557 --
obs0.2575 20418 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→47.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 8 6 3561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023628
X-RAY DIFFRACTIONf_angle_d0.4774944
X-RAY DIFFRACTIONf_dihedral_angle_d12.1072140
X-RAY DIFFRACTIONf_chiral_restr0.041572
X-RAY DIFFRACTIONf_plane_restr0.004636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
3.1001-3.26360.399704.750.35277798
3.2636-3.4680.411390.34270497
3.468-3.73560.31871270.304279598
3.7356-4.11140.30751460.2623278299
4.1114-4.70590.26481310.22062824100
4.7059-5.92710.25421620.2309276099
5.9271-47.790.26361280.2285280699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0858-0.0164-0.10370.03190.02760.1303-0.1583-0.16970.02970.09570.22130.00190.0574-0.0744-0.03481.216-0.19240.00221.0641-0.01310.2033-50.552430.5178-14.6714
20.25040.0055-0.13520.0757-0.03730.1002-0.0143-0.1549-0.12490.1120.06040.05860.6322-0.16880.37881.3293-0.30220.08581.023-0.06150.1623-44.563616.6335-21.9635
31.5430.55351.04630.65440.14791.97-0.2684-0.15190.27350.00090.22390.0751-0.2219-0.2893-0.21621.0358-0.00190.0231.0166-0.05750.2383-40.278932.2936-24.4525
40.64720.3833-0.84350.3665-0.19451.7210.1763-0.0017-0.1705-0.0164-0.1557-0.13450.78280.0276-0.14781.14180.4047-0.07450.91950.06650.3384-13.141426.2426-16.5877
50.6201-0.38620.06810.67520.07410.0388-0.1358-0.1742-0.0830.27410.15680.1310.06820.0196-0.48490.7230.48270.0360.70350.05590.3375-18.842531.9842-18.2832
60.2909-0.11850.1880.1359-0.07360.1218-0.03640.0090.04520.0253-0.0473-0.00230.0050.0531-0.93180.68210.4391-0.0110.59240.00090.2211-11.400531.6038-11.9789
71.22510.653-0.30320.7786-0.2432.72520.2586-0.1328-0.20380.0785-0.2842-0.23710.39310.97310.04971.10620.4806-0.03111.2776-0.02340.4587-8.565728.8714-4.5461
81.05861.6054-0.00092.4338-0.02672.18620.0616-0.2264-0.2585-0.17260.1524-0.45690.79180.38270.25751.30310.66290.19731.21320.21510.5871-0.093921.7258-7.0037
90.6324-0.31250.27741.5676-0.69960.6297-0.1949-0.2359-0.00980.44010.18790.1983-0.0464-0.0949-0.55121.21480.59120.20870.90040.27660.6915-6.465117.732-6.4545
102.0045-1.09650.74592.0654-0.30230.2850.26130.1051-0.2064-0.04290.0909-0.12860.24480.14671.49441.12450.7266-0.07541.40420.18261.08172.36812.1864-9.5797
111.31-0.65520.61792.392-0.33940.39660.0767-0.2137-0.36530.1154-0.077-0.32550.08660.12670.70610.84520.4721-0.05040.68210.23310.6966-7.193913.5007-1.7703
120.12910.2548-0.03860.54230.02320.25480.02150.0775-0.1347-0.263-0.0898-0.359-0.0557-0.00330.2461.9550.86590.06191.08830.03760.7408-6.84246.7351-13.9858
130.1229-0.0481-0.02480.0669-0.08210.18690.01850.0242-0.058-0.1680.00440.03970.01970.0210.43222.19810.6044-0.11480.7655-0.01240.6013-13.89614.6962-25.6419
140.0171-0.088-0.00960.4586-0.12060.44320.03270.0729-0.0093-0.0384-0.0827-0.01790.11750.1079-0.97591.41170.73040.10290.94750.02730.4466-16.872113.3026-10.831
150.78250.01460.42790.32260.46780.89160.1016-0.1272-0.18170.1378-0.12070.04890.4486-0.0397-0.75461.10430.3814-0.01220.5350.06470.2226-18.284323.4831-20.178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 112 through 164 )
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 282 )
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 361 )
4X-RAY DIFFRACTION4chain 'B' and (resid 112 through 128 )
5X-RAY DIFFRACTION5chain 'B' and (resid 129 through 143 )
6X-RAY DIFFRACTION6chain 'B' and (resid 144 through 164 )
7X-RAY DIFFRACTION7chain 'B' and (resid 165 through 198 )
8X-RAY DIFFRACTION8chain 'B' and (resid 199 through 215 )
9X-RAY DIFFRACTION9chain 'B' and (resid 216 through 234 )
10X-RAY DIFFRACTION10chain 'B' and (resid 235 through 249 )
11X-RAY DIFFRACTION11chain 'B' and (resid 250 through 262 )
12X-RAY DIFFRACTION12chain 'B' and (resid 263 through 286 )
13X-RAY DIFFRACTION13chain 'B' and (resid 287 through 315 )
14X-RAY DIFFRACTION14chain 'B' and (resid 316 through 337 )
15X-RAY DIFFRACTION15chain 'B' and (resid 338 through 361 )

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