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- PDB-8icy: DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + THYMIDINE-5'-TRIP... -

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Basic information

Entry
Database: PDB / ID: 8icy
TitleDNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + THYMIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DTTP AND MNCL2
Components
  • DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3')
  • DNA (5'-D(*TP*CP*TP*AP*AP*TP*GP*T)-3')
  • PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))
KeywordsTRANSFERASE/DNA / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION / DNA REPAIR / NUCLEOTIDYLTRANSFERASE / COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA) / 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
: / THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 3.1 Å
AuthorsPelletier, H. / Sawaya, M.R.
Citation
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.
#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: Characterization of the Metal Ion-Binding HHH Motifs in Human DNA Polymerase Beta by X-Ray Structural Analysis
Authors: Pelletier, H. / Sawaya, M.R.
#5: Journal: Science / Year: 1994
Title: Polymerase Structures and Mechanism
Authors: Pelletier, H.
#6: 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.
#7: 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
DepositionDec 15, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Dec 15, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.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.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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
T: DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3')
P: DNA (5'-D(*TP*CP*TP*AP*AP*TP*GP*T)-3')
A: PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6767
Polymers43,0933
Non-polymers5834
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.792, 57.617, 48.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 2 types, 2 molecules TP

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


Mass: 2434.643 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*CP*TP*AP*AP*TP*GP*T)-3')


Mass: 2416.615 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))


Mass: 38241.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06746

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Non-polymers , 4 types, 137 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsA POSSIBLE PHYSIOLOGICAL SUBSTRATE FOR POL BETA IS A DNA GAP, WHERE THE LENGTH OF THE GAP CAN RANGE ...A POSSIBLE PHYSIOLOGICAL SUBSTRATE FOR POL BETA IS A DNA GAP, WHERE THE LENGTH OF THE GAP CAN RANGE FROM ONE TO SIX NUCLEOTIDES, AND THE DOWNSTREAM END OF THE DNA GAP IS 5'-PHOSPHORYLATED. IN ORDER TO CREATE VARIOUS GAPPED-DNA SUBSTRATES FOR USE IN POL BETA-DNA CO-CRYSTALLIZATION ATTEMPTS, THE AUTHORS HAD TO ANNEAL THREE DIFFERENT OLIGONUCLEOTIDES TOGETHER PRIOR TO CRYSTALLIZATION: (1) A RELATIVELY LONG (14 TO 20 MER) OLIGONUCLEOTIDE THAT WAS TO SERVE AS THE TEMPLATE, (2) ONE SHORTER (5 OR 6 MER) OLIGONUCLEOTIDE THAT WAS TO SERVE AS THE PRIMER, AND (3) ANOTHER SHORTER (4 TO 10 MER) OLIGONUCLEOTIDE THAT WAS 5'-PHOSPHORYLATED AND WAS TO SERVE AS THE DOWNSTREAM OLIGONUCLEOTIDE. DNA SEQUENCES CORRESPONDING TO THE TEMPLATE, THE PRIMER, AND THE DOWNSTREAM OLIGONUCLEOTIDE FOR THE CRYSTAL STRUCTURE PRESENTED HERE ARE: 5'-CATTAGAAAGGGAAGCGCCG-3' (20-MER), 5'-CGGCGC-3' (6-MER), AND 5'-PO4-TCTAATG-3' (7-MER), RESPECTIVELY, WHERE "5'-PO4" INDICATES THAT THE 5' TERMINUS OF THIS OLIGONUCLEOTIDE IS 5'-PHOSPHORYLATED. HOWEVER, AN UNEXPECTED POL BETA-DNA COMPLEX RESULTED FROM THE CO-CRYSTALLIZATION ATTEMPTS SO THAT WHAT WAS ORIGINALLY INTENDED TO BE THE 5'-PHOSPHORYLATED DOWNSTREAM OLIGONUCLEOTIDE IS BOUND WHERE THE PRIMER STRAND WAS EXPECTED TO BIND (SEE REFERENCE 1). IN ADDITION, A MAJORITY OF THE GAPPED-DNA SUBSTRATE (THAT IS, SIX BASE PAIRS OF TEMPLATE-PRIMER TETHERED TO A FLEXIBLE, SINGLE-STRANDED DNA GAP) IS TOO DISORDERED TO BE OBSERVABLE IN THE CRYSTAL STRUCTURE, ALTHOUGH IT IS NEVERTHELESS THOUGHT TO BE PRESENT IN THE CRYSTAL LATTICE (SEE REFERENCE 1). THE END RESULT IS THAT, ALTHOUGH THE AFOREMENTIONED TEMPLATE IS STILL REFERRED TO AS THE TEMPLATE IN THE STRUCTURES PRESENTED HERE, THE AFOREMENTIONED "DOWNSTREAM OLIGONUCLEOTIDE" IS NOW CALLED THE "PRIMER" -- BY ANALOGY WITH PREVIOUSLY REPORTED POL BETA-DNA-DDCTP TERNARY COMPLEX STRUCTURES (SEE ENTRIES 2BPF AND 2BPG AND REFERENCE 8). ONLY THE DNA NUCLEOTIDES THAT WERE VISIBLE IN THE STRUCTURE ARE INCLUDED IN THE SEQRES SECTION BELOW.

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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: 3 Å3/Da / Density % sol: 58.4 %
Crystal growpH: 6.5
Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE ...Details: THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DTTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Crystal
*PLUS
Density % sol: 58.4 %
Crystal grow
*PLUS
Temperature: 298 K / 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 RU200
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Feb 4, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 9053 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rsym value: 5.9
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 1.4 % / Rsym value: 14.1 / % possible all: 94
Reflection
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 20 Å / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.2 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
TNT5-Drefinement
SDMSdata reduction
SDMSdata scaling
TNTV. 5-Dphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 8ICB

8icb


Resolution: 3.1→20 Å / σ(F): 0 / Stereochemistry target values: STANDARD TNT /
RfactorNum. reflection% reflection
obs0.168 9053 94 %
Solvent computationSolvent model: MOEWS / Bsol: 428.3 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 309 23 133 3088
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01929970.02
X-RAY DIFFRACTIONt_angle_deg3.140523
X-RAY DIFFRACTIONt_dihedral_angle_d191803
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.016730.02
X-RAY DIFFRACTIONt_gen_planes0.0063950.02
X-RAY DIFFRACTIONt_it5.630046
X-RAY DIFFRACTIONt_nbd0.0281630.02
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 20 Å / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg3.1
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19

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