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- PDB-3v7k: Co-crystal structure of K72E variant of rat polymerase beta: Enzy... -

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Basic information

Entry
Database: PDB / ID: 3v7k
TitleCo-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex
Components
  • DNA (5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3')
  • DNA (5'-D(P*CP*AP*AP*AP*CP*TP*CP*AP*CP*AP*A)-3')
  • DNA polymerase beta
KeywordsTransferase/DNA / Protein-DNA complex / repair polymerase / Transferase-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / inflammatory response / apoptotic process / DNA damage response / enzyme binding / protein-containing complex / DNA binding / 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, N-terminal domain-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 ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-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 lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.271 Å
AuthorsRangarajan, S. / Jaeger, J.
CitationJournal: To be Published
Title: Crystallographic studies of K72E mutant DNA polymerase explain loss of lyase function and reveal changes in the overall conformational state of the polymerase domain
Authors: Rangarajan, S. / Gridley, C.L. / Firbank, S. / Dalal, S. / Sweasy, J.B. / Jaeger, J.
History
DepositionDec 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,9277
Polymers44,8353
Non-polymers924
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-44 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.464, 75.508, 117.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase beta /


Mass: 39058.371 Da / Num. of mol.: 1 / Mutation: K72E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Polb / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P06766, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: DNA chain DNA (5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3')


Mass: 2481.652 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*CP*AP*AP*AP*CP*TP*CP*AP*CP*AP*A)-3')


Mass: 3295.203 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, NaCl, Glycerol, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2011
RadiationMonochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.271→30.3 Å / Num. all: 201278 / Num. obs: 23840 / % possible obs: 91.49 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rsym value: 0.062 / Net I/σ(I): 38.1
Reflection shellResolution: 2.2711→2.3279 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.627 / Rsym value: 0.649 / % possible all: 72.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.271→30.3 Å / SU ML: 0.73 / σ(F): 0.09 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1899 8.71 %random
Rwork0.2253 ---
obs0.2298 21799 91.49 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.995 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3239 Å2-0 Å20 Å2
2--12.6877 Å20 Å2
3----0.8635 Å2
Refinement stepCycle: LAST / Resolution: 2.271→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 372 4 127 3156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093145
X-RAY DIFFRACTIONf_angle_d1.2734316
X-RAY DIFFRACTIONf_dihedral_angle_d18.8991238
X-RAY DIFFRACTIONf_chiral_restr0.084472
X-RAY DIFFRACTIONf_plane_restr0.004503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2711-2.32790.36231100.29731199X-RAY DIFFRACTION79
2.3279-2.39080.31121290.27051382X-RAY DIFFRACTION90
2.3908-2.46110.30951320.27771394X-RAY DIFFRACTION91
2.4611-2.54050.29641330.27731397X-RAY DIFFRACTION92
2.5405-2.63130.3781400.28471423X-RAY DIFFRACTION93
2.6313-2.73660.29421390.24961441X-RAY DIFFRACTION94
2.7366-2.8610.31141430.25231488X-RAY DIFFRACTION97
2.861-3.01180.26551450.23251509X-RAY DIFFRACTION98
3.0118-3.20030.26541440.23371508X-RAY DIFFRACTION98
3.2003-3.4470.28981470.23191504X-RAY DIFFRACTION97
3.447-3.79330.31611060.30591099X-RAY DIFFRACTION70
3.7933-4.34090.28611270.2021348X-RAY DIFFRACTION86
4.3409-5.46380.23571500.17121579X-RAY DIFFRACTION100
5.4638-30.32190.23391540.18861629X-RAY DIFFRACTION97

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