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- PDB-4o9m: Human DNA polymerase beta complexed with adenylated tetrahydrofur... -

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Basic information

Entry
Database: PDB / ID: 4o9m
TitleHuman DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA
Components
  • (5'-D(P*GP*TP*CP*GP*G)-3');
  • DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / Lyase / Aprataxin / Adenylated Tetrahydrofuran / TRANSFERASE-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 / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair ...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 / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / DNA-templated DNA replication / 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 / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / 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 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 / 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
Chem-2RW / DNA / DNA (> 10) / DNA/RNA hybrid / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsCaglayan, M. / Batra, V.K. / Sassa, A. / Prasad, R. / Wilson, S.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Role of polymerase beta in complementing aprataxin deficiency during abasic-site base excision repair.
Authors: Caglayan, M. / Batra, V.K. / Sassa, A. / Prasad, R. / Wilson, S.H.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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
B: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
C: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3')
D: (5'-D(P*GP*TP*CP*GP*G)-3');
A: DNA polymerase beta
D: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S)-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5547
Polymers47,9814
Non-polymers5733
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-43 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.627, 78.873, 54.324
Angle α, β, γ (deg.)90.00, 105.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules BC

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


Mass: 4853.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized oligoncleotide
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3')


Mass: 3350.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized oligoncleotide

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DNA/RNA hybrid / Protein , 2 types, 2 molecules DA

#3: DNA/RNA hybrid (5'-D(P*GP*TP*CP*GP*G)-3');


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized oligoncleotide
#4: 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 / Plasmid: pWL11 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP56
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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Non-polymers , 3 types, 303 molecules D

#5: Chemical ChemComp-2RW / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S)-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 527.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O12P2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-Tris, 350 mM Sodium Acetate, 16% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 21, 2013 / Details: Viramax
RadiationMonochromator: Viramax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.295→23.51 Å / Num. all: 19178 / Num. obs: 19178 / % possible obs: 96.4 % / Observed criterion σ(F): -4 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P66

2p66


Resolution: 2.295→23.51 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1924 10.03 %
Rwork0.1934 --
obs0.2002 19178 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.295→23.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 649 36 300 3590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133436
X-RAY DIFFRACTIONf_angle_d1.2044766
X-RAY DIFFRACTIONf_dihedral_angle_d21.0511346
X-RAY DIFFRACTIONf_chiral_restr0.069522
X-RAY DIFFRACTIONf_plane_restr0.004495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2953-2.35270.34561000.2728906X-RAY DIFFRACTION70
2.3527-2.41620.34681180.25331065X-RAY DIFFRACTION86
2.4162-2.48720.34521420.24821261X-RAY DIFFRACTION98
2.4872-2.56740.28281370.24071261X-RAY DIFFRACTION100
2.5674-2.65910.34841420.2291263X-RAY DIFFRACTION100
2.6591-2.76540.34931400.24541267X-RAY DIFFRACTION100
2.7654-2.8910.3531430.251274X-RAY DIFFRACTION99
2.891-3.04310.34991430.27391259X-RAY DIFFRACTION99
3.0431-3.23330.34291440.21721268X-RAY DIFFRACTION100
3.2333-3.48220.22721430.17861272X-RAY DIFFRACTION100
3.4822-3.83130.22281420.17071297X-RAY DIFFRACTION100
3.8313-4.38260.24961390.16311269X-RAY DIFFRACTION99
4.3826-5.50990.21421440.16321285X-RAY DIFFRACTION100
5.5099-23.51170.18751470.15661307X-RAY DIFFRACTION100

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