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- PDB-8dwd: Adenine glycosylase MutY variant E43S in complex with DNA contain... -

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Basic information

Entry
Database: PDB / ID: 8dwd
TitleAdenine glycosylase MutY variant E43S in complex with DNA containing d(8-oxo-G) paired with an AP site generated by the enzyme acting on purine
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*AP*(ORP)P*GP*TP*CP*T)-3')
KeywordsHYDROLASE/DNA / Protein-DNA complex / DNA repair / Base Excision Repair / Apurinic/Apyrimidinic / 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
ACETATE ION / 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: 1.68 Å
AuthorsRusselburg, L.P. / Demir, M. / David, S.S. / Horvath, M.P.
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: To Be Published
Title: Structural Basis for Base Engagement and Stereochemistry Revealed by Alteration of Catalytic Residue Glu43 in DNA Repair Glycosylase MutY
Authors: Russelburg, L.P. / Demir, M. / Cedeno, K. / David, S.S. / Horvath, M.P.
History
DepositionAug 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release

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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(*TP*GP*TP*CP*CP*AP*(ORP)P*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8537
Polymers48,3623
Non-polymers4914
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-61 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.740, 85.920, 140.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenine DNA glycosylase


Mass: 41731.559 Da / Num. of mol.: 1 / Mutation: E43S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83847

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DNA chain , 2 types, 2 molecules BC

#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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*CP*CP*AP*(ORP)P*GP*TP*CP*T)-3')


Mass: 3207.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 218 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.38 Å3/Da / Density % sol: 48.2 % / Description: yellow, hexagonal rod
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, calcium acetate, ethylene glycol, Tris-HCl, beta-mercaptoethanol
Temp details: Ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2021
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→43 Å / Num. obs: 100381 / % possible obs: 99.6 % / Redundancy: 6.76 % / Biso Wilson estimate: 30.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.41
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 7 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 7356 / CC1/2: 0.313 / % possible all: 98.5

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Processing

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

6u7t


Resolution: 1.68→42.96 Å / SU ML: 0.2698 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3631
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 2520 2.51 %
Rwork0.2224 97859 -
obs0.2229 100379 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.79 Å2
Refinement stepCycle: LAST / Resolution: 1.68→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 423 14 214 3324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843270
X-RAY DIFFRACTIONf_angle_d1.02894566
X-RAY DIFFRACTIONf_chiral_restr0.0516512
X-RAY DIFFRACTIONf_plane_restr0.0094512
X-RAY DIFFRACTIONf_dihedral_angle_d17.52341214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.39051410.38875434X-RAY DIFFRACTION98.38
1.71-1.750.3411400.35655312X-RAY DIFFRACTION99.43
1.75-1.790.35581290.33785463X-RAY DIFFRACTION99.01
1.79-1.830.34031440.31285363X-RAY DIFFRACTION98.78
1.83-1.870.29451480.31565484X-RAY DIFFRACTION99.96
1.87-1.920.34081440.31235378X-RAY DIFFRACTION99.1
1.92-1.980.34471330.3075476X-RAY DIFFRACTION99.88
1.98-2.040.31281390.29335425X-RAY DIFFRACTION99.57
2.04-2.120.32931390.27015446X-RAY DIFFRACTION99.66
2.12-2.20.27321400.25065478X-RAY DIFFRACTION99.98
2.2-2.30.30141600.25515376X-RAY DIFFRACTION99.78
2.3-2.420.24521430.24715458X-RAY DIFFRACTION99.93
2.42-2.570.24231430.24855435X-RAY DIFFRACTION99.89
2.57-2.770.24381420.23695476X-RAY DIFFRACTION99.96
2.77-3.050.28931410.23885443X-RAY DIFFRACTION99.96
3.05-3.490.2291310.19185474X-RAY DIFFRACTION99.96
3.49-4.40.16891240.17425468X-RAY DIFFRACTION100
4.4-42.960.20821390.18345470X-RAY DIFFRACTION99.96
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)
12.95970472668-0.376842682233-0.404095813650.965617396819-0.2623410826270.4342932699110.2682143049481.526559226380.169339586303-0.160279058324-0.194214531729-0.0349803330493-0.10628968862-0.0955962933493-0.03337733297290.2413097718160.06725765544940.05330217092830.3252282864770.01433686177430.19023474808312.84978993982.299298892523.03677421979
20.4035910313330.0420070274578-0.004174230779730.08259616131630.001146229378760.1863507753670.0768216105501-0.6105169012030.3288279470450.2529980755590.0991026428724-0.2565040549690.03409815999340.3958731673480.002649271971350.488594726738-0.0381238780394-0.05732136173030.568247573308-0.1286438519290.34990523353220.78256939657.7026291913937.3312536403
30.231496585756-0.2704943600570.04424139238110.3263394281350.002467027018770.1580472637140.07136969809830.00779307748863-0.308403173339-0.116619407339-0.128973960813-0.1336911876650.350114755950.1392138884451.56244950802E-50.3599522662550.0120511719085-0.006709767981280.2549969023330.02033478932010.34280835451120.1469532461-3.994544703516.1449263192
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 8:228 or resid 401 or resid 403))AA - D8 - 4031
22((chain A) and (resid 229:360 or resid 402 or resid 404))AA - E229 - 404222
33((chain B and resid 1:11) or (chain C and resid 12:22))B - CF - G1 - 22

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