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- PDB-5cys: Structure of the enzyme-product complex resulting from TDG action... -

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Basic information

Entry
Database: PDB / ID: 5cys
TitleStructure of the enzyme-product complex resulting from TDG action on a GcaC mismatch
Components
  • (DNA (28-MER)) x 2
  • G/T mismatch-specific thymine DNA glycosylase
Keywordshydrolase/dna / protein-DNA complex / 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
ACETIC ACID / DNA / DNA (> 10) / G/T mismatch-specific thymine DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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)GM051074 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Characterizing the enzyme-product complexes of thymine DNA glycosylase using crystallography and NMR
Authors: Malik, S.S. / Varney, K.M. / Pozharski, E. / Drohat, A.C.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: G/T mismatch-specific thymine DNA glycosylase
C: DNA (28-MER)
D: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2514
Polymers40,1913
Non-polymers601
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-25 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.887, 53.804, 81.245
Angle α, β, γ (deg.)90.00, 96.07, 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 / hTDG


Mass: 23070.670 Da / Num. of mol.: 1 / 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, thymine-DNA glycosylase
#2: DNA chain DNA (28-MER)


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


Mass: 8473.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.28357 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28357 Å / Relative weight: 1
ReflectionResolution: 2.45→32.84 Å / Num. obs: 15396 / Biso Wilson estimate: 69.07 Å2
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.7 % / Rejects: _

Resolution (Å)Mean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible allRmerge(I) obs
2.45-2.550.6805717140.3381.6396.9
8.82-32.8518.916703560.9990.02398.10.046

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→32.84 Å / Cor.coef. Fo:Fc: 0.9658 / Cor.coef. Fo:Fc free: 0.9406 / SU R Cruickshank DPI: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.514 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.242
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 786 5.11 %RANDOM
Rwork0.1654 ---
obs0.1689 15396 98.35 %-
Displacement parametersBiso mean: 75.25 Å2
Baniso -1Baniso -2Baniso -3
1--2.016 Å20 Å24.4536 Å2
2---0.05 Å20 Å2
3---2.066 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: LAST / Resolution: 2.45→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 1135 4 207 2904
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012922HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.044203HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d843SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes298HARMONIC5
X-RAY DIFFRACTIONt_it2922HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion23.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion378SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3125SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.62 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3637 113 4.33 %
Rwork0.2317 2499 -
all0.2375 2612 -
obs--98.35 %
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)
1-1.3415-8.26911.61276.5397-5.913410.3429-0.05790.5602-0.00230.1421-0.3247-0.991-0.05951.70140.38251.17150.1019-0.17220.48690.1040.142826.2538-16.841831.4392
24.1535-1.98040.5745.7348-1.69013.2931-0.0431-0.2234-0.20360.57830.02910.34790.178-0.09010.0140.6524-0.0494-0.0865-0.0246-0.0314-0.067510.6717-6.354829.3568
315.3481-15.5563-5.54811.1628.456512.4441-0.4439-1.0444-0.2220.31060.12150.36310.1784-0.16770.32240.61710.10580.01940.2861-0.0093-0.09937.5733-5.139939.2763
44.6214-0.3597-1.11064.0615-0.581810.29290.06660.0395-0.5579-0.4378-0.260.50870.03580.34310.19340.57230.0434-0.0845-0.1652-0.0375-0.15414.3379-8.841821.2167
50.2221.95962.83541.80431.08975.6398-0.22270.3931-0.1176-0.86060.20160.43310.3879-0.11780.02110.71360.0017-0.2201-0.0524-0.00460.08016.6464-4.246716.4587
69.86068.3971-1.78214.8685-2.80691.5242-0.44590.17380.6205-0.4816-0.0334-0.28720.14970.31970.47940.98490.0132-0.0562-0.0637-0.0196-0.244613.32620.05729.003
70.71540.7103-1.56323.404-0.90193.8509-0.12610.120.3026-1.3189-0.04270.3996-0.02330.3760.16880.83580.066-0.2226-0.0281-0.0189-0.01029.50084.647916.3099
83.8108-0.6966-1.116.15230.40220.4873-0.20430.25610.8740.59880.08360.5948-0.0052-0.24720.12070.88740.0963-0.18030.0493-0.07180.065310.82569.034630.081
98.4824-2.1361-0.236800.41922.5989-0.1643-0.00930.33150.1201-0.13780.59080.1822-0.61570.3020.70850.2039-0.2890.2428-0.0260.6144-7.57963.950523.3033
105.50093.3292-3.500517.8289-5.131715.09150.1780.036-0.42770.20030.47761.51350.2395-0.9665-0.65571.371-0.2050.02190.72180.2556-0.261628.543113.14243.5989
1111.56012.2685-2.92590.0004-0.54467.08870.12410.04140.42520.05380.1617-0.89540.47390.9304-0.28581.0206-0.0844-0.07540.62270.1912-0.122133.13418.887121.6148
123.5646-6.3138-5.667312.85088.68959.07210.1025-0.7532-0.050.5877-0.23380.19960.05990.26270.13140.7310.0178-0.44420.03490.0503-0.256625.39753.333339.4485
132.1501-0.0897-2.04389.9716-2.664624.22620.2254-0.1375-0.080.74080.11740.041-0.88310.4451-0.34281.1185-0.0466-0.43530.02230.0485-0.127835.8491-5.741363.5815
144.45262.10821.4589.5466-3.65581.50950.3492-0.28290.11050.0066-0.0768-0.1927-0.27330.5076-0.27231.3165-0.0188-0.28440.0681-0.0326-0.230236.0353-3.99760.5969
159.72871.0027-2.45837.124-1.631810.2768-0.25790.15790.632-0.9280.2607-0.2981-0.85481.2155-0.00280.8181-0.1474-0.10270.13770.0587-0.255828.31727.141322.0429
165.6294.11211.581116.36434.5166.98780.17680.3338-1.3625-0.0540.42750.18250.24390.7342-0.60431.3204-0.0028-0.01910.63010.1965-0.18732.277411.3876-2.0984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|109 - A|123 }
2X-RAY DIFFRACTION2{ A|124 - A|170 }
3X-RAY DIFFRACTION3{ A|171 - A|175 }
4X-RAY DIFFRACTION4{ A|176 - A|215 }
5X-RAY DIFFRACTION5{ A|216 - A|235 }
6X-RAY DIFFRACTION6{ A|236 - A|244 }
7X-RAY DIFFRACTION7{ A|245 - A|277 }
8X-RAY DIFFRACTION8{ A|278 - A|293 }
9X-RAY DIFFRACTION9{ A|294 - A|305 }
10X-RAY DIFFRACTION10{ C|1 - C|7 }
11X-RAY DIFFRACTION11{ C|8 - C|11 }
12X-RAY DIFFRACTION12{ C|12 - C|17 }
13X-RAY DIFFRACTION13{ C|18 - C|28 }
14X-RAY DIFFRACTION14{ D|1 - D|13 }
15X-RAY DIFFRACTION15{ D|14 - D|24 }
16X-RAY DIFFRACTION16{ D|25 - D|28 }

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