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- PDB-7s9j: Crystal Structure of DNA Polymerase Beta with Fapy-dG base-paired... -

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Basic information

Entry
Database: PDB / ID: 7s9j
TitleCrystal Structure of DNA Polymerase Beta with Fapy-dG base-paired with a dC
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*(FAP)P*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*CP*AP*TP*GP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsDNA BNDING PROTEIN/DNA / Fapy-dG / duplex DNA / polymerase Beta / non-mutagenic / DNA BNDING PROTEIN-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / response to hyperoxia / lymph node development / salivary gland morphogenesis / somatic hypermutation of immunoglobulin genes / spleen development / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to gamma radiation / spindle microtubule / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / intrinsic apoptotic signaling pathway in response to DNA damage / neuron apoptotic process / response to ethanol / microtubule binding / in utero embryonic development / DNA-directed DNA polymerase / damaged DNA binding / microtubule / DNA-directed DNA polymerase activity / Ub-specific processing proteases / lyase activity / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsFreudenthal, B.D. / Ryan, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication.
Authors: Ryan, B.J. / Yang, H. / Bacurio, J.H.T. / Smith, M.R. / Basu, A.K. / Greenberg, M.M. / Freudenthal, B.D.
History
DepositionSep 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: DNA polymerase beta
T: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*(FAP)P*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*CP*AP*TP*GP*CP*GP*C)-3')
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8188
Polymers47,7264
Non-polymers924
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-69 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.383, 79.494, 54.885
Angle α, β, γ (deg.)90.000, 105.716, 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, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 38241.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli)
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 4927.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*CP*AP*TP*GP*CP*GP*C)-3')


Mass: 3020.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3')


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 468 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.91→25 Å / Num. obs: 53238 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.23 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.122 / Net I/σ(I): 11
Reflection shellResolution: 1.91→5.17 Å / Num. unique obs: 1730 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ISB

3isb


Resolution: 1.91→24.86 Å / SU ML: 0.2483 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 3276 6.15 %
Rwork0.1879 49962 -
obs0.1911 53238 77.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.43 Å2
Refinement stepCycle: LAST / Resolution: 1.91→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 633 4 464 3694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983369
X-RAY DIFFRACTIONf_angle_d1.02364667
X-RAY DIFFRACTIONf_chiral_restr0.0693513
X-RAY DIFFRACTIONf_plane_restr0.0061495
X-RAY DIFFRACTIONf_dihedral_angle_d23.54481317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.940.3787390.3645682X-RAY DIFFRACTION23.82
1.94-1.970.4017580.2926867X-RAY DIFFRACTION31.19
1.97-20.3206690.271097X-RAY DIFFRACTION38.74
2-2.040.3264930.25671349X-RAY DIFFRACTION49.06
2.04-2.070.2991040.23711561X-RAY DIFFRACTION55.95
2.07-2.110.23831240.22111787X-RAY DIFFRACTION64.02
2.11-2.160.26141280.22651845X-RAY DIFFRACTION66.84
2.16-2.20.29721270.22742009X-RAY DIFFRACTION70.68
2.2-2.250.28591290.2122029X-RAY DIFFRACTION73.85
2.25-2.310.26591400.21232176X-RAY DIFFRACTION78.03
2.31-2.370.28351490.21472322X-RAY DIFFRACTION82.42
2.37-2.440.29631610.22442477X-RAY DIFFRACTION87.79
2.44-2.520.3141700.23052556X-RAY DIFFRACTION91.88
2.52-2.610.33051750.21792658X-RAY DIFFRACTION94.84
2.61-2.720.2631760.21682677X-RAY DIFFRACTION96.42
2.72-2.840.34451850.23452711X-RAY DIFFRACTION97.02
2.84-2.990.28161790.22792722X-RAY DIFFRACTION97.45
2.99-3.180.29371720.22432722X-RAY DIFFRACTION97.21
3.18-3.420.2231850.16732732X-RAY DIFFRACTION97.72
3.42-3.760.18741780.15432722X-RAY DIFFRACTION97.94
3.77-4.310.18691790.13632762X-RAY DIFFRACTION98.46
4.31-5.410.15271880.13632765X-RAY DIFFRACTION98.53
5.42-24.860.15531680.14022734X-RAY DIFFRACTION97.84

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