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- PDB-4z3a: Acetate-free structure of the enzyme-product complex resulting fr... -

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Basic information

Entry
Database: PDB / ID: 4z3a
TitleAcetate-free structure of the enzyme-product complex resulting from TDG action on a GU 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


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
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: 1.72 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)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
DepositionMar 31, 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 / 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)


Theoretical massNumber of molelcules
Total (without water)40,1913
Polymers40,1913
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-27 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.158, 53.565, 81.390
Angle α, β, γ (deg.)90.00, 95.06, 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: 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMicroheterogeneity at residues 17 in chain D, this structure contains both anomeric forms of the ...Microheterogeneity at residues 17 in chain D, this structure contains both anomeric forms of the abasic nucleotide, ORP and AAB at 0.5 occupancy.

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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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M Ammonium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.72→32.24 Å / Num. obs: 43547 / % possible obs: 97.7 % / Redundancy: 8.8 % / Biso Wilson estimate: 31.54 Å2 / Net I/σ(I): 6.64
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 4.63 % / Rmerge(I) obs: 0.044 / Mean I/σ(I) obs: 0.57 / % possible all: 92.4

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Processing

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

4fnc


Resolution: 1.72→32.24 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1732 4.76 %RANDOM
Rwork0.199 ---
obs0.2 42189 96.9 %-
Displacement parametersBiso mean: 49.76 Å2
Baniso -1Baniso -2Baniso -3
1--10.6153 Å20 Å2-0.0359 Å2
2---0.0559 Å20 Å2
3---10.6711 Å2
Refine analyzeLuzzati coordinate error obs: 0.357 Å
Refinement stepCycle: LAST / Resolution: 1.72→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 1135 0 185 2870
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012949HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994229HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d861SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes34HARMONIC2
X-RAY DIFFRACTIONt_gen_planes297HARMONIC5
X-RAY DIFFRACTIONt_it2949HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion21.4
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_contact3136SEMIHARMONIC4
LS refinement shellResolution: 1.72→1.76 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.2567 146 5.02 %
Rwork0.2627 2760 -
obs--96.87 %
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)
19.58683.53353.72743.43749.42049.66590.02130.42060.944-0.23450.2831-0.1405-0.72120.5797-0.30440.45790.0305-0.0390.1910.11410.232928.6568-12.454837.0737
23.7934-0.09881.52692.7974-0.44024.04530.26350.1214-0.42880.0926-0.22240.36490.48430.0646-0.04110.2578-0.0312-0.01920.0728-0.04180.206211.8307-11.405424.3755
33.794-2.43540.70745.7949-0.99432.6263-0.1499-0.1899-0.02390.68540.02590.28290.08160.01390.1240.2523-0.02120.00110.0435-0.0080.109213.1978-4.525434.076
413.5469-1.9185-0.99096.39072.78098.8057-0.235-0.6457-0.31330.36910.16030.57120.4606-0.20390.07470.3624-0.02290.09590.15280.05510.1896.964-5.81139.4347
53.4249-0.4663-1.04112.9928-0.74625.2321-0.05290.0218-0.18980.2667-0.13350.53520.4251-0.1890.18640.2853-0.04830.02020.0936-0.03960.22819.5899-9.453126.9492
610.86894.36690.7976.7444-0.55814.4930.17680.06-0.345-0.448-0.4067-0.30910.49010.77330.22990.30340.0476-0.01410.2203-0.01020.019219.4153-7.395212.9549
71.8872-1.44840.2285.5736-0.33413.32070.04470.2654-0.0303-0.5813-0.22920.4998-0.0208-0.15880.18450.2269-0.0022-0.14060.106-0.04830.12437.5010.560313.9443
83.6692-1.73551.37281.8399-0.86362.7277-0.1505-0.1318-0.06760.2428-0.0340.3877-0.2658-0.24120.18450.14830.0353-0.0366-0.0031-0.06670.12348.64856.864628.3123
93.3621.377-2.94883.4266-4.123214.5585-0.3050.8210.35-0.71670.1943-0.27020.25950.4740.11070.3864-0.1541-0.07010.34510.14070.149628.12579.229219.4267
101.19750.29743.07944.4745-2.805615.02050.2534-0.1284-0.09330.7695-0.1634-0.3104-0.9310.4086-0.090.4783-0.019-0.23040.16460.02430.180335.5904-5.716262.1753
112.27610.24780.14553.527-2.48098.12480.26060.04620.07310.8483-0.0945-0.2829-0.85910.5135-0.1660.4899-0.0179-0.15790.11760.00850.217235.7086-3.418257.5504
121.9871.7257-3.17680.0958-2.366411.0460.16240.34170.2071-0.9689-0.15810.058-0.2931.2237-0.00430.5966-0.08750.03530.45930.16320.187628.66349.217112.2948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|105 - A|116 }
2X-RAY DIFFRACTION2{ A|117 - A|142 }
3X-RAY DIFFRACTION3{ A|143 - A|169 }
4X-RAY DIFFRACTION4{ A|170 - A|176 }
5X-RAY DIFFRACTION5{ A|177 - A|198 }
6X-RAY DIFFRACTION6{ A|199 - A|216 }
7X-RAY DIFFRACTION7{ A|217 - A|269 }
8X-RAY DIFFRACTION8{ A|270 - A|300 }
9X-RAY DIFFRACTION9{ C|1 - C|16 }
10X-RAY DIFFRACTION10{ C|17 - C|28 }
11X-RAY DIFFRACTION11{ D|1 - D|15 }
12X-RAY DIFFRACTION12{ D|16 - D|28 }

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