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- PDB-4z7z: Structure of the enzyme-product complex resulting from TDG action... -

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Basic information

Entry
Database: PDB / ID: 4z7z
TitleStructure of the enzyme-product complex resulting from TDG action on a GT mismatch in the presence of excess base
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


G/U mismatch-specific uracil-DNA glycosylase activity / thymine-DNA glycosylase / G/T mismatch-specific thymine-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 / base-excision repair, AP site formation / sodium ion binding / depyrimidination / DNA N-glycosylase activity ...G/U mismatch-specific uracil-DNA glycosylase activity / thymine-DNA glycosylase / G/T mismatch-specific thymine-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 / base-excision repair, AP site formation / sodium ion binding / depyrimidination / 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 / protein kinase C binding / epigenetic regulation of gene expression / 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 / magnesium ion binding / negative regulation of transcription by RNA polymerase II / 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: 1.83 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)R01-GM72711 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
DepositionApr 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 13, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
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)40,3135
Polymers40,1913
Non-polymers1222
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-22 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.729, 53.460, 82.033
Angle α, β, γ (deg.)90.00, 95.54, 90.00
Int Tables number5
Space group name H-MC121

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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 / Fragment: UNP residues 111-308
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.) 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)

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Non-polymers , 3 types, 207 molecules

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACY / ACETIC ACID


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


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
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: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→39.26 Å / Num. obs: 34165 / % possible obs: 98.5 % / Redundancy: 8.8 % / Biso Wilson estimate: 34.67 Å2 / Net I/σ(I): 10.2
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 3 % / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 0.4 / % possible all: 91.5

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
Aimless0.5.4data scaling
PDB_EXTRACT3.15data extraction
Blu-Icedata collection
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNC

4fnc


Resolution: 1.83→39.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0.009 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.139 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1660 4.88 %RANDOM
Rwork0.193 ---
obs0.195 34036 98.1 %-
Displacement parametersBiso mean: 55.85 Å2
Baniso -1Baniso -2Baniso -3
1--13.586 Å20 Å21.8657 Å2
2--2.0191 Å20 Å2
3---11.5669 Å2
Refine analyzeLuzzati coordinate error obs: 0.441 Å
Refinement stepCycle: LAST / Resolution: 1.83→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 894 249 205 2883
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012927HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994202HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d857SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes297HARMONIC5
X-RAY DIFFRACTIONt_it2927HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion21.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion376SEMIHARMONIC5
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_contact3189SEMIHARMONIC4
LS refinement shellResolution: 1.83→1.89 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.2667 167 5.66 %
Rwork0.257 2781 -
obs--98.07 %
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)
111.43540.3822-8.40011.67555.375822.96570.20.28550.13960.07690.1157-0.44540.27870.3439-0.31570.41980.10150.03550.52430.20350.148326.7746-16.776835.0298
24.4486-1.30521.81644.1929-2.31755.52240.0874-0.1633-0.32930.2029-0.12380.36020.54430.10730.03640.3883-0.04450.04040.0913-0.02980.105811.5015-11.229125.1003
32.359-1.4538-1.14964.1977-1.2673.6266-0.2041-0.3039-0.11941.2120.05650.02670.21460.17270.14750.49840.0203-0.00040.13370.01620.068413.9079-6.30433.8523
42.08790.47070.65614.43681.78267.3797-0.0504-0.33410.00731.2054-0.00150.74180.2515-0.50190.05190.4028-0.04630.2090.15670.01040.19163.1478-5.145634.1539
57.7083-2.4489-0.93296.7809-4.75486.8796-0.04510.044-0.08160.0713-0.2972-0.0523-0.24110.98260.34230.50390.00930.05170.3450.03260.047820.3378-10.059620.9139
610.39752.1676-0.46784.6817-1.43594.24340.25240.0854-0.0991-0.3341-0.4627-0.10090.23770.76380.21030.48160.01310.07090.28170.00170.023518.161-7.951312.9642
74.5940.48430.9184.2277-0.492.948-0.15560.1603-0.18-0.51290.03190.53320.146-0.28810.12370.3276-0.0304-0.04120.1468-0.040.17274.4817-4.948217.1027
86.10191.04960.27853.56251.37613.6686-0.07230.39990.1888-0.5831-0.0079-0.0099-0.35930.40920.08020.4709-0.02550.04080.16650.01660.024613.26171.94069.7446
97.2692-4.9248-0.93560-4.32775.12660.03610.20960.4613-1.1769-0.11440.0405-0.30840.09810.0783-0.00320.0926-0.02380.18920.06610.25869.42399.686213.6228
103.24461.69550.40965.11713.73818.7514-0.04020.3194-0.0619-0.33850.01880.54120.2386-0.39950.02140.3574-0.0794-0.10030.1637-0.02010.19060.4713-0.399512.3809
111.97770.28953.4052.19440.85865.3265-0.07570.02590.2620.2739-0.08530.1537-0.09060.33630.1610.30880.0133-0.00880.1242-0.0040.070617.4145.84227.0717
126.3860.78651.85071.78380.30854.188-0.1299-0.31020.27880.3877-0.07640.6636-0.2993-0.64250.20630.26890.07070.06640.1009-0.05980.1871.4216.970727.1247
139.0894-2.456-1.98584.5977-1.28683.75660.3958-0.38540.2903-0.0503-0.08721.3394-0.0131-0.4977-0.30860.8124-0.00250.17610.53680.15360.042525.331717.77710.1219
148.4073.96274.394511.4545.1798.63920.0560.5655-1.229-0.10370.376-0.00960.41380.4243-0.43210.6093-0.07490.09350.71230.10290.022129.02596.57569.9875
156.3953-0.8739-0.07375.487-0.29229.9490.2975-0.23680.08570.3752-0.2726-0.1892-0.26730.8782-0.02490.31650.0048-0.14060.28980.02480.001826.51495.59734.5797
161.55060.34360.96668.7114-3.345813.33610.2298-0.05930.00850.6376-0.1254-0.2389-1.06630.4397-0.10450.62250.0375-0.20680.2226-0.01050.20733.6836-5.751864.2077
173.21480.2092-0.24585.3731-2.77877.20990.38440.11120.10230.7912-0.2271-0.305-0.64520.5292-0.15730.53250.01-0.11430.1065-0.00060.143133.5574-3.421858.0817
182.2252.1227-5.38323.2518-4.214812.71480.09390.170.228-0.7057-0.1229-0.0698-0.08040.97240.02890.5961-0.0936-0.03690.47580.14230.141827.33029.35712.3343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|111 - A|117 }
2X-RAY DIFFRACTION2{ A|118 - A|144 }
3X-RAY DIFFRACTION3{ A|145 - A|162 }
4X-RAY DIFFRACTION4{ A|163 - A|190 }
5X-RAY DIFFRACTION5{ A|191 - A|200 }
6X-RAY DIFFRACTION6{ A|201 - A|216 }
7X-RAY DIFFRACTION7{ A|217 - A|233 }
8X-RAY DIFFRACTION8{ A|234 - A|247 }
9X-RAY DIFFRACTION9{ A|248 - A|257 }
10X-RAY DIFFRACTION10{ A|258 - A|267 }
11X-RAY DIFFRACTION11{ A|268 - A|280 }
12X-RAY DIFFRACTION12{ A|281 - A|303 }
13X-RAY DIFFRACTION13{ C|1 - C|4 }
14X-RAY DIFFRACTION14{ C|5 - C|8 }
15X-RAY DIFFRACTION15{ C|9 - C|17 }
16X-RAY DIFFRACTION16{ C|18 - C|28 }
17X-RAY DIFFRACTION17{ D|1 - D|15 }
18X-RAY DIFFRACTION18{ D|16 - D|28 }

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