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- PDB-6cr3: Ternary complex crystal structure of DNA polymerase Beta with a d... -

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Basic information

Entry
Database: PDB / ID: 6cr3
TitleTernary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
Keywordstranscription/DNA / DNA Polymerase Beta / Conformational Change / enzyme mechanism / LFER / transcription-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
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, 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 / 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 / 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-H84 / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBatra, V.K. / Wilson, S.H.
CitationJournal: Biochemistry / Year: 2018
Title: Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Authors: Batra, V.K. / Oertell, K. / Beard, W.A. / Kashemirov, B.A. / McKenna, C.E. / Goodman, M.F. / Wilson, S.H.
History
DepositionMar 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,52011
Polymers47,7094
Non-polymers8117
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-94 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.874, 79.669, 55.784
Angle α, β, γ (deg.)90.000, 107.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 4844.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pWL-11 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap56
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: 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.) Homo sapiens (human)

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Protein , 1 types, 1 molecules A

#4: Protein DNA polymerase beta


Mass: 38283.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pwl-11 / 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 , 5 types, 506 molecules

#5: Chemical ChemComp-H84 / 2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine / beta, gamma dATP analogue


Mass: 647.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16Br2N5O11P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.31 Å3/Da / Density % sol: 46.76 % / Mosaicity: 1.237 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 16-18% PEG 3350 / PH range: 7.5, 50 mM Imidazole, 350 mM Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 30503 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.088 / Χ2: 1.352 / Net I/σ(I): 10 / Num. measured all: 105442
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.95-2.022.70.57925551.414183
2.02-2.13.20.43631241.379199.6
2.1-2.23.50.33930481.3471100
2.2-2.313.50.28931271.3581100
2.31-2.463.50.23530631.303199.9
2.46-2.653.50.18631001.42199.9
2.65-2.913.50.12931091.3661100
2.91-3.333.60.07231011.26199.9
3.33-4.23.70.04731321.273199.8
4.2-503.60.03931441.432199.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMS

2fms


Resolution: 1.95→23.182 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.35
RfactorNum. reflection% reflection
Rfree0.2266 1995 6.55 %
Rwork0.1748 --
obs0.1782 30442 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.33 Å2 / Biso mean: 27.4564 Å2 / Biso min: 12.09 Å2
Refinement stepCycle: final / Resolution: 1.95→23.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 629 38 499 3780
Biso mean--20.65 33.22 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073400
X-RAY DIFFRACTIONf_angle_d0.8774715
X-RAY DIFFRACTIONf_chiral_restr0.048514
X-RAY DIFFRACTIONf_plane_restr0.005496
X-RAY DIFFRACTIONf_dihedral_angle_d18.0341941
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.947-1.99570.32921130.26331612172577
1.9957-2.04960.27941380.2271964210296
2.0496-2.10990.26651460.212320662212100
2.1099-2.1780.2671430.197420422185100
2.178-2.25570.27681460.196620902236100
2.2557-2.3460.26331460.198120822228100
2.346-2.45260.24381430.194520322175100
2.4526-2.58180.28461450.192720582203100
2.5818-2.74330.2461460.19920782224100
2.7433-2.95470.24431460.20192072221899
2.9547-3.25130.25661450.196320732218100
3.2513-3.72010.19481450.142820802225100
3.7201-4.68070.18911440.134620832227100
4.6807-23.18360.15951490.148521152264100

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