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- PDB-8dw7: DNA glycosylase MutY variant N146S in complex with DNA containing... -

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Basic information

Entry
Database: PDB / ID: 8dw7
TitleDNA glycosylase MutY variant N146S in complex with DNA containing the transition state analog 1N paired with d(8-oxo-G)
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')
KeywordsHYDROLASE/DNA / Protein-DNA complex / DNA repair / transition state / Base Excision Repair / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


adenine glycosylase / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein ...A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Adenine DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsDemir, M. / Russelburg, L.P. / Horvath, M.P. / David, S.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1905304 United States
National Science Foundation (NSF, United States)1905249 United States
National Science Foundation (NSF, United States)1610721 United States
National Science Foundation (NSF, United States)1608934 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism.
Authors: Demir, M. / Russelburg, L.P. / Lin, W.J. / Trasvina-Arenas, C.H. / Huang, B. / Yuen, P.K. / Horvath, M.P. / David, S.S.
History
DepositionJul 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenine DNA glycosylase
B: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
C: DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')
D: Adenine DNA glycosylase
E: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
F: DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,87414
Polymers96,7226
Non-polymers1,1528
Water3,423190
1
A: Adenine DNA glycosylase
B: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
C: DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9377
Polymers48,3613
Non-polymers5764
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Adenine DNA glycosylase
E: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
F: DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9377
Polymers48,3613
Non-polymers5764
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.890, 137.210, 74.160
Angle α, β, γ (deg.)90.000, 101.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Adenine DNA glycosylase / oxoG:A-specific adenine glycosylase


Mass: 41746.574 Da / Num. of mol.: 2 / Mutation: N146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mutY / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83847, adenine glycosylase

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')


Mass: 3423.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')


Mass: 3191.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 198 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 293.13 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, calcium acetate, ethylene glycol, Tris.HCl, b-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11585 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 6, 2019
RadiationMonochromator: Si(111) Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11585 Å / Relative weight: 1
ReflectionResolution: 1.96→72.8 Å / Num. obs: 128636 / % possible obs: 94.7 % / Redundancy: 3.14 % / Biso Wilson estimate: 45.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 0.089
Reflection shellResolution: 1.96→2.01 Å / Num. unique obs: 9334 / CC1/2: 0.102

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U7T

6u7t


Resolution: 1.96→72.8 Å / SU ML: 0.3378 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 3194 2.5 %
Rwork0.203 124537 -
obs0.2038 127731 94.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.2 Å2
Refinement stepCycle: LAST / Resolution: 1.96→72.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5352 844 42 190 6428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01976476
X-RAY DIFFRACTIONf_angle_d1.46349014
X-RAY DIFFRACTIONf_chiral_restr0.08741020
X-RAY DIFFRACTIONf_plane_restr0.0131004
X-RAY DIFFRACTIONf_dihedral_angle_d18.40312352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.990.37891200.38464895X-RAY DIFFRACTION86.23
1.99-2.020.40351360.37065199X-RAY DIFFRACTION89.59
2.02-2.050.36381340.36395272X-RAY DIFFRACTION91.44
2.05-2.090.36651340.33625170X-RAY DIFFRACTION90.85
2.09-2.130.3431490.32865476X-RAY DIFFRACTION93.42
2.13-2.170.31521080.30725361X-RAY DIFFRACTION94.78
2.17-2.210.33371230.29055502X-RAY DIFFRACTION94
2.21-2.260.3821560.31215484X-RAY DIFFRACTION96.07
2.26-2.310.29661360.25775440X-RAY DIFFRACTION93.94
2.31-2.370.31471290.25075553X-RAY DIFFRACTION96.39
2.37-2.430.25681590.24395378X-RAY DIFFRACTION93.61
2.43-2.510.30611230.24315497X-RAY DIFFRACTION96.27
2.51-2.590.28041420.23565460X-RAY DIFFRACTION93.69
2.59-2.680.28661460.23375557X-RAY DIFFRACTION96.69
2.68-2.790.22021290.21475521X-RAY DIFFRACTION96.1
2.79-2.910.27641670.21835499X-RAY DIFFRACTION95.86
2.91-3.070.2331490.20145510X-RAY DIFFRACTION95.51
3.07-3.260.24631380.20095506X-RAY DIFFRACTION95.13
3.26-3.510.24221310.17435514X-RAY DIFFRACTION95.56
3.51-3.860.21361700.17025415X-RAY DIFFRACTION95.65
3.86-4.420.14911360.15215428X-RAY DIFFRACTION93.5
4.42-5.570.19161430.16175362X-RAY DIFFRACTION93.57
5.57-72.80.22281360.19415538X-RAY DIFFRACTION96.1
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)
11.28142892124-0.1377085167660.3381826384231.126329881360.2819660207282.308953463670.03550671010260.001748406313290.0604673385377-0.0275176931456-0.02932370448040.03788959602020.0613810792238-0.185351236314-0.007366698631840.332644172972-0.01103238959960.0113499383040.3827962788530.05699993320110.4905828020672.803366011046.019356964786.46791113992
21.45099988991-0.0684135033404-0.007040333574121.705464619520.07691108686081.459188543790.137618122127-0.438852920012-0.2187267079820.5476643165910.038095961907-0.3352577087560.3369280786240.323099592085-0.17363807340.6960267880910.0368772100384-0.1946233932850.6791511951790.07333726707680.66268695193124.5881638558-2.6158524629134.2689326994
31.92417890909-0.250623726947-0.3121201756551.56199653256-0.5813275507892.212689374450.04457344075080.0821277273538-0.06783459638910.024821334839-0.0446067094898-0.115760489853-0.07272298150.159621063213-0.00280851094960.327632489759-0.0134370353081-0.02459020967070.394787778565-0.0288075241890.39614554702421.7812909109-42.51088463246.49979331104
41.90555264425-0.582034462783-0.2694262182321.830412258870.06492009141631.23365880931-0.0126596604817-0.5403864259610.09324573268310.5456386623620.063153133090.186854668195-0.032719835958-0.279452714899-0.02450824811270.6891298308160.01259145353780.1223222467650.686483906895-0.04100273845560.430013606047-0.771339945057-33.572756710533.238883514
51.059018935710.1704173290750.2210686564092.024751295490.159153377570.839856080020.1737601338640.0608116525475-0.182456047841-0.0504598017122-0.261281133624-0.1691003746480.1526271907970.1460869365120.1023398361670.4438056777220.0356703070696-0.03341322948310.3826431767210.04057436588290.51488922508216.3034501591-0.99692795248711.6925163215
61.6662275197-0.126749324015-0.283801175532.641380779840.2241572882161.240458918660.1945044300740.05513484398790.116219264767-0.117568981649-0.3522750762250.187775923167-0.207839091484-0.1936588883330.1586579645530.4426546131960.0337523000127-0.000846571956580.3954124701-0.02788365901320.4192093512628.12291209837-35.460386923711.6072776139
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and (resid 5:228 or resid 401 or resid 403))AA - D5 - 4031
22(chain A and (resid 229:359))AA229 - 359225 - 352
33(chain D and (resid 4:228 or resid 401 or resid 403))DG - J4 - 4031
44(chain D and (resid 229:360))DG229 - 360226 - 349
55(chain B and (resid 1:11)) or (chain C and (resid 12:22))B - CE - F1 - 22
66(chain E and (resid 1:11)) or (chain F and (resid 12:22))E - FK - L1 - 22

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