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- PDB-1dk2: REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYME... -

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Basic information

Entry
Database: PDB / ID: 1dk2
TitleREFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA
ComponentsDNA POLYMERASE BETA
KeywordsTRANSFERASE / DNA-BINDING / DEOXYRIBOSE 5'-PHOSPHATE LYASE / NUCLEOTIDYLTRANSFERASE
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
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 / Nucleotidyltransferase superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsMaciejewski, M.W. / Prasad, R. / Liu, D.-J. / Wilson, S.H. / Mullen, G.P.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity.
Authors: Maciejewski, M.W. / Liu, D. / Prasad, R. / Wilson, S.H. / Mullen, G.P.
#1: Journal: Biochemistry / Year: 1996
Title: Three-Dimensional Solution Structure of the N-terminal Domain of DNA Polymerase beta and Mapping of the ssDNA Interaction Interface
Authors: Liu, D.-J. / Prasad, R. / Wilson, S.H. / DeRose, E.F. / Mullen, G.P.
#2: Journal: Biochemistry / Year: 1994
Title: Assignments of 1H, 15N, and 13C Resonances for the Backbone and Side Chains of the N-terminal Domain of DNA Polymerase beta. Determination of the Secondary Structure and Tertiary Contacts
Authors: Liu, D.-J. / DeRose, E.F. / Prasad, R. / Wilson, S.H. / Mullen, G.P.
History
DepositionDec 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Apr 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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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)9,5011
Polymers9,5011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100THE SELECTION UTILIZED THE LOWEST ENERGY STRUCTURES WITH NO NOE VIOLATIONS EXCEEDING 0.3 ANGSTROMS AND NO DIHEDRAL VIOLATIONS EXCEEDING 0.3 DEGREES.
RepresentativeModel #10lowest energy

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Components

#1: Protein DNA POLYMERASE BETA / E.C.2.7.7.7


Mass: 9501.103 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PRSET-8K / Production host: Escherichia coli (E. coli) / References: UniProt: P06766, DNA-directed DNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1152D NOESY
2223D 15N-SEPARATED NOESY
1343D 13C-SEPARATED NOESY
143HMQC-J
NMR detailsText: PROTEOLYTIC PROCESSING REMOVES THE N-TERMINAL MET IN A BACTERIAL EXPRESSION SYSTEM (SEE KUMAR ET AL., (1990) J. BIOL. CHEM. 265, 2124-2131).

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Sample preparation

Details
Solution-IDContents
12.8 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N,13C; 5MM TRIS- D11; 400MM NACL
22 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11; 100MM NACL
34 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N; 5MM TRIS-D11; 400MM NACL
42.8 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87) U-15N,13C; 5MM TRIS- D11; 400MM NACL
51.4 MM RAT DNA POLYMERASE BETA N-TERMINAL DOMAIN (2-87); 5MM TRIS-D11; 400MM NACL
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1400 mM NACL 6.7AMBIENT 300 K
2100 mM NACL 6.8AMBIENT 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE GN500GEGN5005001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4.3VARIANcollection
Felix95HARE, BIOSYMprocessing
XEASY1.3.13BARTELSdata analysis
DYANA1.5GUENTERTstructure solution
X-PLOR4BRUNGERrefinement
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: THE NMR RESTRAINTS INCLUDED 921 USEFUL NOE DETERMINED UPPER DISTANCE RESTRAINTS, 41 HYDROGEN BONDS, AND 135 PHI AND CHI TORSION ANGLE RESTRAINTS. STRUCTURES WERE CALCULATED IN THE PROGRAM ...Details: THE NMR RESTRAINTS INCLUDED 921 USEFUL NOE DETERMINED UPPER DISTANCE RESTRAINTS, 41 HYDROGEN BONDS, AND 135 PHI AND CHI TORSION ANGLE RESTRAINTS. STRUCTURES WERE CALCULATED IN THE PROGRAM DYANA USING TORSION ANGLE DYNAMICS. THE CALCULATION STARTED WITH 100 RANDOMIZED STRUCTURES. THE 50 STRUCTURES WITH THE LOWEST TARGET FUNCTION WERE THEN REFINED WITHIN XPLOR USING SIMULATED ANNEALING. THE 25 LOWEST ENERGY STRUCTURAL CONFORMERS WERE SELECTED TO REPRESENT THE ENSEMBLE.THE 25 REFINED STRUCTURAL CONFORMERS DISPLAYED NO NOE VIOLATIONS >0.3 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS >3 DEGREES. THE MINIMIZED AVERAGE STRUCTURE WAS CALCULATED FROM THE MEAN POSITION OF THE COORDINATES FOR THE 25 STRUCTURAL CONFORMERS AND WAS REFINED BY POWELL ENERGY MINIMIZATION IN XPLOR USING FULL NMR RESTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: THE SELECTION UTILIZED THE LOWEST ENERGY STRUCTURES WITH NO NOE VIOLATIONS EXCEEDING 0.3 ANGSTROMS AND NO DIHEDRAL VIOLATIONS EXCEEDING 0.3 DEGREES.
Conformers calculated total number: 100 / Conformers submitted total number: 25

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