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- PDB-4xeg: Structure of the enzyme-product complex resulting from TDG action... -

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Basic information

Entry
Database: PDB / ID: 4xeg
TitleStructure of the enzyme-product complex resulting from TDG action on a G/hmU mismatch
Components
  • (DNA (28-MER)) x 2
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsHYDROLASE/DNA / DNA glycosylase / abasic site / enzyme-product complex / 5-hydroxymethyluracil / HYDROLASE-DNA complex
Function / homology
Function and homology information


G/T mismatch-specific thymine-DNA glycosylase activity / thymine-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / DNA N-glycosylase activity / sodium ion binding / SUMO binding ...G/T mismatch-specific thymine-DNA glycosylase activity / thymine-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / DNA N-glycosylase activity / sodium ion binding / SUMO binding / mismatched DNA binding / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / DNA demethylation / chloride ion binding / regulation of embryonic development / epigenetic regulation of gene expression / 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 / protein kinase C binding / transcription coregulator activity / base-excision repair / PML body / : / double-stranded DNA binding / DNA-binding transcription factor binding / damaged DNA binding / nucleic acid binding / protein domain specific binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / DNA 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 / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DNA / DNA (> 10) / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsPozharski, E. / Malik, S.S. / Drohat, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM072711 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.
Authors: Malik, S.S. / Coey, C.T. / Varney, K.M. / Pozharski, E. / Drohat, A.C.
History
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

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Assembly

Deposited unit
A: G/T mismatch-specific thymine DNA glycosylase
C: DNA (28-MER)
D: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4958
Polymers40,1913
Non-polymers3045
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-21 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.199, 53.393, 82.220
Angle α, β, γ (deg.)90.000, 95.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 23070.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDG / Production host: Escherichia coli (E. coli) / References: UniProt: Q13569, thymine-DNA glycosylase

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (28-MER)


Mass: 8646.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (28-MER)


Mass: 8473.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Non-polymers , 3 types, 305 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% (w/v) PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.72→39.14 Å / Num. obs: 40036 / % possible obs: 97.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.016 / Net I/σ(I): 23.8 / Num. measured all: 266180
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.72-1.753.80.9181.4502713320.7610.49162.1
9.09-39.146.60.016101194329510.00797.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDS0.1.26data reduction
PHASERphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FNC

4fnc


Resolution: 1.72→39.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.258 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 2016 5 %RANDOM
Rwork0.1882 38012 --
obs0.1904 38012 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.21 Å2 / Biso mean: 38.544 Å2 / Biso min: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.03 Å2
2--0.02 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.72→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 1135 20 304 3013
Biso mean--50.92 47.36 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0162967
X-RAY DIFFRACTIONr_bond_other_d0.0020.022236
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.5964255
X-RAY DIFFRACTIONr_angle_other_deg1.19635207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8475205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95224.24773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2915291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.905157
X-RAY DIFFRACTIONr_chiral_restr0.1150.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212544
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02669
X-RAY DIFFRACTIONr_mcbond_it3.4283.27805
X-RAY DIFFRACTIONr_mcbond_other3.4113.258801
X-RAY DIFFRACTIONr_mcangle_it4.2584.8831004
LS refinement shellResolution: 1.718→1.763 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 107 -
Rwork0.393 2041 -
all-2148 -
obs--71.29 %

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