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- PDB-2rba: Structure of Human Thymine DNA Glycosylase Bound to Abasic and Un... -

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Basic information

Entry
Database: PDB / ID: 2rba
TitleStructure of Human Thymine DNA Glycosylase Bound to Abasic and Undamaged DNA
Components
  • DNA (5'-D(*DCP*DAP*DGP*DCP*DTP*DCP*DTP*DGP*DTP*DAP*DCP*DGP*DTP*DGP*DAP*DGP*DCP*DAP*DGP*DTP*DGP*DGP*DA)-3')
  • DNA (5'-D(*DCP*DCP*DAP*DCP*DTP*DGP*DCP*DTP*DCP*DAP*(3DR)P*DGP*DTP*DAP*DCP*DAP*DGP*DAP*DGP*DCP*DTP*DGP*DT)-3')
  • G/T mismatch-specific thymine DNA glycosylase
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / DNA damage / DNA repair / Glycosidase / Hydrolase / Nucleus / 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 / : / sodium ion binding / DNA N-glycosylase activity ...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 / : / sodium ion binding / DNA N-glycosylase activity / mismatched DNA binding / SUMO binding / Displacement of DNA glycosylase by APEX1 / uracil DNA N-glycosylase activity / chloride ion binding / regulation of embryonic development / SUMOylation of DNA damage response and repair proteins / epigenetic regulation of gene expression / 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 / nucleic acid binding / damaged DNA 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
DNA / DNA (> 10) / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsMaiti, A. / Pozharski, E. / Drohat, A.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition.
Authors: Maiti, A. / Morgan, M.T. / Pozharski, E. / Drohat, A.C.
History
DepositionSep 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*DCP*DAP*DGP*DCP*DTP*DCP*DTP*DGP*DTP*DAP*DCP*DGP*DTP*DGP*DAP*DGP*DCP*DAP*DGP*DTP*DGP*DGP*DA)-3')
D: DNA (5'-D(*DCP*DCP*DAP*DCP*DTP*DGP*DCP*DTP*DCP*DAP*(3DR)P*DGP*DTP*DAP*DCP*DAP*DGP*DAP*DGP*DCP*DTP*DGP*DT)-3')
A: G/T mismatch-specific thymine DNA glycosylase
B: G/T mismatch-specific thymine DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)60,1554
Polymers60,1554
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.133, 162.133, 56.142
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: DNA chain DNA (5'-D(*DCP*DAP*DGP*DCP*DTP*DCP*DTP*DGP*DTP*DAP*DCP*DGP*DTP*DGP*DAP*DGP*DCP*DAP*DGP*DTP*DGP*DGP*DA)-3')


Mass: 7121.597 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DCP*DCP*DAP*DCP*DTP*DGP*DCP*DTP*DCP*DAP*(3DR)P*DGP*DTP*DAP*DCP*DAP*DGP*DAP*DGP*DCP*DTP*DGP*DT)-3')


Mass: 6892.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein G/T mismatch-specific thymine DNA glycosylase


Mass: 23070.670 Da / Num. of mol.: 2 / Fragment: Core domain
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, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8 mg/ml protein and 20% molar excess DNA duplex in 10mM Tris-HCL, 100 mM NaCl, 0.5mM DTT. Reservoir: 20% PEG 3350, 0.2M K/Na tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HCL11
2NaCl11
3DTT11
4PEG 335012
5K/Na tartrate tetrahydrate12

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.91837 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. all: 21137 / Num. obs: 21137 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 87.2 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 25.5
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1 / Num. unique all: 2031 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1wyw, SUMO removed

1wyw


Resolution: 2.79→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 35.695 / SU ML: 0.314 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.642 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27629 1048 5.1 %RANDOM
Rwork0.22965 ---
obs0.23211 19458 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.074 Å2
Baniso -1Baniso -2Baniso -3
1--4.52 Å2-2.26 Å20 Å2
2---4.52 Å20 Å2
3---6.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.353 Å0.642 Å
Refinement stepCycle: LAST / Resolution: 2.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 929 0 0 3845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214132
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2722.2625635
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.625362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86423.731134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.54215540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6141516
X-RAY DIFFRACTIONr_chiral_restr0.170.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022730
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.290.22285
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3380.22612
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9781.51851
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6622928
X-RAY DIFFRACTIONr_scbond_it1.83932881
X-RAY DIFFRACTIONr_scangle_it2.9844.52707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.79→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 71 -
Rwork0.313 1190 -
obs--82.96 %
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)
111.7362.1910.71217.91370.19074.7971-0.17920.28060.40040.0517-0.06770.32950.29110.13340.247-0.3433-0.0480.0867-0.1145-0.0579-0.6205-21.006867.18528.9164
27.37774.9075-0.78019.1255-0.68574.10370.1282-0.37850.79430.2534-0.1940.70830.01190.02340.0658-0.2852-0.07610.0072-0.35580.0185-0.2116-53.999644.223-2.6299
321.579916.9812-26.486834.6056-22.773636.01610.60281.8799-0.83550.4344-1.2229-0.3002-1.76530.68560.62010.11610.49520.21191.0736-0.0615-1.2766-7.05557.895-19.8544
422.0189-6.2633-9.191522.81663.27111.35610.63533.5681-1.7748-3.10340.175-0.88940.7456-0.8575-0.81030.1131-0.26260.26720.4526-0.7103-0.7925-19.227751.4489-6.1421
511.687311.05620.969719.84650.03990.16251.0633-0.4248-2.08760.92450.301-1.37150.68250.0437-1.36440.5945-0.2591-0.26970.49970.23320.649-36.473638.737510.3405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC123 - 30419 - 200
2X-RAY DIFFRACTION2BD123 - 30419 - 200
3X-RAY DIFFRACTION3CA1 - 61 - 6
4X-RAY DIFFRACTION3DB17 - 2217 - 22
5X-RAY DIFFRACTION4CA7 - 127 - 12
6X-RAY DIFFRACTION4DB11 - 1611 - 16
7X-RAY DIFFRACTION5CA13 - 2213 - 22
8X-RAY DIFFRACTION5DB1 - 101 - 10

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