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- PDB-2d07: Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase -

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Basic information

Entry
Database: PDB / ID: 2d07
TitleCrystal Structure of SUMO-3-modified Thymine-DNA Glycosylase
Components
  • G/T mismatch-specific thymine DNA glycosylase
  • Ubiquitin-like protein SMT3B
KeywordsHYDROLASE
Function / homology
Function and homology information


thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / SUMO is proteolytically processed / base-excision repair, AP site formation / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...thymine-DNA glycosylase / G/T mismatch-specific thymine-DNA glycosylase activity / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / SUMO is proteolytically processed / base-excision repair, AP site formation / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / depyrimidination / sodium ion binding / Vitamin D (calciferol) metabolism / DNA N-glycosylase activity / SUMO binding / mismatched DNA binding / Displacement of DNA glycosylase by APEX1 / SUMOylation of SUMOylation proteins / uracil DNA N-glycosylase activity / SUMOylation of RNA binding proteins / SUMO transferase activity / chloride ion binding / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / regulation of embryonic development / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / hippocampal mossy fiber to CA3 synapse / epigenetic regulation of gene expression / protein kinase C binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / GABA-ergic synapse / transcription coregulator activity / SUMOylation of intracellular receptors / base-excision repair / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / double-stranded DNA binding / DNA-binding transcription factor binding / damaged DNA binding / nucleic acid binding / protein domain specific binding / ubiquitin protein ligase binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / magnesium ion binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes / Uracil DNA glycosylase family 2 / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Uracil-DNA glycosylase-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes / Uracil DNA glycosylase family 2 / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Uracil-DNA glycosylase-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 2 / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBaba, D. / Maita, N. / Jee, J.G. / Uchimura, Y. / Saitoh, H. / Sugasawa, K. / Hanaoka, F. / Tochio, H. / Hiroaki, H. / Shirakawa, M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase
Authors: Baba, D. / Maita, N. / Jee, J.G. / Uchimura, Y. / Saitoh, H. / Sugasawa, K. / Hanaoka, F. / Tochio, H. / Hiroaki, H. / Shirakawa, M.
History
DepositionJul 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G/T mismatch-specific thymine DNA glycosylase
B: Ubiquitin-like protein SMT3B


Theoretical massNumber of molelcules
Total (without water)36,8012
Polymers36,8012
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.481, 75.931, 50.527
Angle α, β, γ (deg.)90.00, 114.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein G/T mismatch-specific thymine DNA glycosylase / TDG


Mass: 26177.049 Da / Num. of mol.: 1 / Fragment: central region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q13569, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Protein Ubiquitin-like protein SMT3B / Sentrin-2 / Ubiquitin-related protein SUMO-3 / HSMT3


Mass: 10623.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT-E1E2S2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61956
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.5M sodium malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 21361 / % possible obs: 100 % / Redundancy: 7.4 % / Rsym value: 0.066
Reflection shellResolution: 2.1→2.2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WYW

1wyw


Resolution: 2.1→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.241 1043 -
Rwork0.208 --
all-21343 -
obs-21342 100 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 0 104 2381
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.191
X-RAY DIFFRACTIONc_dihedral_angle_d22.53
X-RAY DIFFRACTIONc_improper_angle_d0.751
LS refinement shellResolution: 2.1→2.17 Å
RfactorNum. reflection% reflection
Rfree0.298 119 -
Rwork0.23 --
obs-2128 100 %

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