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- PDB-1zqu: DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED I... -

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Basic information

Entry
Database: PDB / ID: 1zqu
TitleDNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR
ComponentsDNA POLYMERASE BETA
KeywordsNUCLEOTIDYLTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION / DNA REPAIR
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 / pyrimidine dimer repair / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / response to hyperoxia / lymph node development / salivary gland morphogenesis / somatic hypermutation of immunoglobulin genes / spleen development / base-excision repair, gap-filling / 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 / 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 / microtubule / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / 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, 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 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.6 Å
AuthorsPelletier, H. / Sawaya, M.R.
Citation
Journal: Biochemistry / Year: 1996
Title: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.
Authors: Pelletier, H. / Sawaya, M.R.
#1: Journal: To be Published
Title: Crystal Structures of Human DNA Polymerase Beta Complexed with Nicked and Gapped DNA Substrates
Authors: Sawaya, M.R. / Rawson, T. / Wilson, S.H. / Kraut, J. / Pelletier, H.
#2: Journal: To be Published
Title: The Role of Thumb Movement and Template Bending in Polymerase Fidelity
Authors: Pelletier, H.
#3: Journal: Biochemistry / Year: 1996
Title: Crystal Structures of Human DNA Polymerase Beta Complexed with DNA; Implications for Catalytic Mechanism, Processivity, and Fidelity
Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J.
#4: Journal: Biochemistry / Year: 1996
Title: A Structural Basis for Metal Ion Mutagenicity and Nucleotide Selectivity in Human DNA Polymerase Beta
Authors: Pelletier, H. / Sawaya, M.R. / Wolfle, W. / Wilson, S.H. / Kraut, J.
#5: Journal: Biochemistry / Year: 1996
Title: Characterization of the Metal Ion-Binding HHH Motifs in Human DNA Polymerase Beta by X-Ray Structural Analysis
Authors: Pelletier, H. / Sawaya, M.R.
#6: Journal: Science / Year: 1994
Title: Polymerase Structures and Mechanism
Authors: Pelletier, H.
#7: Journal: Science / Year: 1994
Title: Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template-Primer, and ddCTP
Authors: Pelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J.
#8: Journal: Science / Year: 1994
Title: Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism
Authors: Sawaya, M.R. / Pelletier, H. / Kumar, A. / Wilson, S.H. / Kraut, J.
History
DepositionApr 19, 1996Processing site: BNL
Revision 1.0Nov 15, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA POLYMERASE BETA


Theoretical massNumber of molelcules
Total (without water)28,7751
Polymers28,7751
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.785, 63.255, 37.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

21A-468-

HOH

31A-477-

HOH

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Components

#1: Protein DNA POLYMERASE BETA


Mass: 28774.527 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 31-KD DOMAIN (RESIDUES 88 - 335)
Source method: isolated from a genetically manipulated source
Details: SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: POL / Gene (production host): POL / Production host: Escherichia coli (E. coli) / References: UniProt: P06766, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPLEASE NOTE THAT THIS ENTRY IS ONLY THE 31 KD DOMAIN (RESIDUES 88 - 335) AND THE N-TERMINAL 8 KD ...PLEASE NOTE THAT THIS ENTRY IS ONLY THE 31 KD DOMAIN (RESIDUES 88 - 335) AND THE N-TERMINAL 8 KD DOMAIN IS NOT PRESENT IN THIS STRUCTURE.

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.5
Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION ...Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A CRYSTAL OF THE C-TERMINAL 31-KD DOMAIN OF RAT DNA POL BETA (SEE ENTRY 1BPB AND REFERENCE 9) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115-17 %PEG33501reservoir
20.1 Mcitrate1reservoir
350 mM1reservoiror 50mM Li2SO4NaCl

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Feb 5, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 9098 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.073 / Net I/σ(I): 5.6
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.159 / % possible all: 91
Reflection
*PLUS
Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 91 % / Rmerge(I) obs: 0.159

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Processing

Software
NameVersionClassification
TNT5-Drefinement
SDMSdata reduction
SDMSdata scaling
TNTV. 5-Dphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 1BPB

1bpb


Resolution: 2.6→20 Å / σ(F): 0 / Stereochemistry target values: STANDARD TNT /
Num. reflection% reflection
obs9098 96 %
Solvent computationSolvent model: MOEWS AND KRETSINGER (STANDARD TNT) / Bsol: 322.2 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 0 105 2040
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01819770.02
X-RAY DIFFRACTIONt_angle_deg2.626553
X-RAY DIFFRACTIONt_dihedral_angle_d221190
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.022540.02
X-RAY DIFFRACTIONt_gen_planes0.0082870.02
X-RAY DIFFRACTIONt_it5.519776
X-RAY DIFFRACTIONt_nbd0.0241010.02
Software
*PLUS
Name: TNT / Version: 5-D / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg22

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