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- PDB-5tvq: Mouse Tdp2 catalytic domain bound to SUMO2 -

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Basic information

Entry
Database: PDB / ID: 5tvq
TitleMouse Tdp2 catalytic domain bound to SUMO2
Components
  • Small ubiquitin-related modifier 2
  • Tyrosyl-DNA phosphodiesterase 2
KeywordsHYDROLASE / hydrolase/DNA / dna repair / endonuclease/exonuclease/phosphatase (EEP) domain / hydrolase-dna complex
Function / homology
Function and homology information


SUMO is proteolytically processed / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA damage response and repair proteins / tyrosyl-RNA phosphodiesterase activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins ...SUMO is proteolytically processed / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA damage response and repair proteins / tyrosyl-RNA phosphodiesterase activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / 5'-tyrosyl-DNA phosphodiesterase activity / SUMOylation of intracellular receptors / Nonhomologous End-Joining (NHEJ) / Formation of Incision Complex in GG-NER / Processing of DNA double-strand break ends / positive regulation of protein sumoylation / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / SUMO transferase activity / aggresome / ubiquitin-like protein ligase binding / protein sumoylation / neuron development / nuclear retinoid X receptor binding / protein localization / PML body / protein tag activity / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / manganese ion binding / single-stranded DNA binding / endonuclease activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Ubiquitin homologues / Ubiquitin domain profile. ...Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Small ubiquitin-related modifier 2 / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSchellenberg, M.J. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01ES102765 United States
CitationJournal: Science / Year: 2017
Title: ZATT (ZNF451)-mediated resolution of topoisomerase 2 DNA-protein cross-links.
Authors: Schellenberg, M.J. / Lieberman, J.A. / Herrero-Ruiz, A. / Butler, L.R. / Williams, J.G. / Munoz-Cabello, A.M. / Mueller, G.A. / London, R.E. / Cortes-Ledesma, F. / Williams, R.S.
History
DepositionNov 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
A: Tyrosyl-DNA phosphodiesterase 2
B: Small ubiquitin-related modifier 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8414
Polymers38,7422
Non-polymers992
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-15 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.838, 106.838, 56.585
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Tyrosyl-DNA phosphodiesterase 2 / Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ...Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / TRAF and TNF receptor-associated protein


Mass: 28905.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdp2, Ttrap / Production host: Escherichia coli (E. coli)
References: UniProt: Q9JJX7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Protein Small ubiquitin-related modifier 2 / SUMO-2 / SMT3 homolog 2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 9836.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sumo2, Smt3b, Smt3h2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61957
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM MES, 18% PEG 8000, 200 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 15578 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 74.46 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Χ2: 1.009 / Net I/av σ(I): 26.276 / Net I/σ(I): 13.2 / Num. measured all: 110520
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.814.30.50949870.8340.2750.5811.265100
1.81-1.894.30.3650400.9080.1950.4111.429100
1.89-1.974.40.24350420.9540.1310.2771.598100
1.97-2.074.40.17650750.9750.0940.21.93599.9
2.07-2.24.40.13550710.9830.0720.1542.21599.9
2.2-2.384.40.11250850.9860.060.1282.45899.9
2.38-2.614.30.09551050.9890.0510.1092.79999.9
2.61-2.994.20.07651160.9920.0410.0873.32899.5
2.99-3.774.10.05651710.9950.0310.0653.48499.7
3.77-404.30.03453760.9980.0180.0391.98398.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GZ1

4gz1


Resolution: 2.35→29.748 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.18
RfactorNum. reflection% reflection
Rfree0.2309 749 4.82 %
Rwork0.1861 --
obs0.1883 15550 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 233.19 Å2 / Biso mean: 105.9607 Å2 / Biso min: 56.85 Å2
Refinement stepCycle: final / Resolution: 2.35→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 5 37 2659
Biso mean--100.65 79.64 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162688
X-RAY DIFFRACTIONf_angle_d1.093633
X-RAY DIFFRACTIONf_chiral_restr0.057399
X-RAY DIFFRACTIONf_plane_restr0.007473
X-RAY DIFFRACTIONf_dihedral_angle_d14.0181626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3437-2.52460.35061500.30792906305699
2.5246-2.77850.34861470.249429573104100
2.7785-3.18010.25661490.210129873136100
3.1801-4.00510.24921530.20929623115100
4.0051-29.75060.20181500.15742989313998

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