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- PDB-4jgc: Human TDG N140A mutant IN A COMPLEX WITH 5-carboxylcytosine (5caC) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4jgc
TitleHuman TDG N140A mutant IN A COMPLEX WITH 5-carboxylcytosine (5caC)
Components
  • G/T mismatch-specific thymine DNA glycosylase
  • oligonucleotide
  • oligonucleotide containing 5-carboxylcytosine
KeywordsHYDROLASE/DNA / 5-carboxylcytosine / thymine DNA glycosylase / DNA modification / DNA 5mC oxidation / epigenetic regulation / DNA demethylation / HYDROLASE-DNA complex
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 / 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 ...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 / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / epigenetic regulation of gene expression / 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
Chem-1RT / DNA / DNA (> 10) / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.582 Å
AuthorsHashimoto, H. / Zhang, X. / Cheng, X.
CitationJournal: Dna Repair / Year: 2013
Title: Activity and crystal structure of human thymine DNA glycosylase mutant N140A with 5-carboxylcytosine DNA at low pH.
Authors: Hashimoto, H. / Zhang, X. / Cheng, X.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Sep 20, 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
A: G/T mismatch-specific thymine DNA glycosylase
C: oligonucleotide
D: oligonucleotide containing 5-carboxylcytosine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3034
Polymers40,1483
Non-polymers1551
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-24 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.486, 53.555, 81.902
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23027.645 Da / Num. of mol.: 1 / Fragment: UNP residues 111-308 / Mutation: N140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDG / Plasmid: pXC1057 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13569, thymine-DNA glycosylase
#2: DNA chain oligonucleotide


Mass: 8646.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesis
#3: DNA chain oligonucleotide containing 5-carboxylcytosine


Mass: 8473.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesis
#4: Chemical ChemComp-1RT / 4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid


Mass: 155.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Compound details5-CARBOXY-2'-DEOXYCYTIDINE MONOPHOSPHATE in the DNA GOT CLEAVED INTO 5-CARBOXYLCYTOSINE BASE AND 2- ...5-CARBOXY-2'-DEOXYCYTIDINE MONOPHOSPHATE in the DNA GOT CLEAVED INTO 5-CARBOXYLCYTOSINE BASE AND 2-DEOXY-5-PHOSPHONO-RIBOSE

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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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: 30% polyethylene glycol (PEG) 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, temperature 289K

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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: Nov 30, 2011
Details: ROSENBAUM-ROCK MONOCHROMATO HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.582→45.56 Å / Num. obs: 11604 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.7
Reflection shellResolution: 2.582→2.68 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2 / Num. unique all: 922 / % possible all: 73.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FNC

4fnc


Resolution: 2.582→45.56 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2833 578 5 %RANDOM
Rwork0.2298 ---
obs0.2324 11567 91.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.336 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-31.1096 Å2-0 Å2-3.7997 Å2
2---10.6579 Å20 Å2
3----20.4517 Å2
Refinement stepCycle: LAST / Resolution: 2.582→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 1133 11 22 2690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192853
X-RAY DIFFRACTIONf_angle_d1.1964097
X-RAY DIFFRACTIONf_dihedral_angle_d22.9161131
X-RAY DIFFRACTIONf_chiral_restr0.05451
X-RAY DIFFRACTIONf_plane_restr0.007331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5824-2.84230.39851220.38342232X-RAY DIFFRACTION76
2.8423-3.25350.36471390.27942753X-RAY DIFFRACTION92
3.2535-4.09860.29111560.22772974X-RAY DIFFRACTION99
4.0986-45.56910.23541610.19393030X-RAY DIFFRACTION100

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