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- PDB-2bpg: STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA... -

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Basic information

Entry
Database: PDB / ID: 2bpg
TitleSTRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP
Components
  • DNA (5'-D(*CP*GP*GP*CP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*G)-3')
  • DNA POLYMERASE BETA
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / TRANSFERASE-DNA COMPLEX
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, 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 / 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
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA polymerase beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 3.6 Å
AuthorsPelletier, H. / Sawaya, M.R. / Kumar, A. / Wilson, S.H. / Kraut, J.
Citation
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.
#1: 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
DepositionMay 19, 1994Deposition site: BNL / Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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(*GP*GP*GP*CP*GP*CP*CP*G)-3')
P: DNA (5'-D(*CP*GP*GP*CP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*G)-3')
D: DNA (5'-D(*CP*GP*GP*CP*GP*CP*C)-3')
A: DNA POLYMERASE BETA
B: DNA POLYMERASE BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8409
Polymers85,9146
Non-polymers9273
Water724
1
T: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*G)-3')
P: DNA (5'-D(*CP*GP*GP*CP*GP*CP*C)-3')
A: DNA POLYMERASE BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4325
Polymers42,9573
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-20 kcal/mol
Surface area18310 Å2
MethodPISA
2
C: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*G)-3')
D: DNA (5'-D(*CP*GP*GP*CP*GP*CP*C)-3')
B: DNA POLYMERASE BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4084
Polymers42,9573
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-10 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.300, 56.800, 86.700
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ASN B 245 - GLU B 249 OMEGA = 329.09 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATIO
DetailsTHE FIRST COMPLEX IN THE ASYMMETRIC UNIT HAS BEEN ASSIGNED CHAIN IDENTIFIERS A, T, AND P FOR THE PROTEIN MOLECULE, TEMPLATE, AND PRIMER, RESPECTIVELY, AND THE SECOND COMPLEX IN THE ASYMMETRIC UNIT HAS BEEN ASSIGNED CHAIN IDENTIFIERS B, C, AND D FOR THE SECOND PROTEIN MOLECULE, TEMPLATE, AND PRIMER, RESPECTIVELY.

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Components

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DNA chain , 2 types, 4 molecules TCPD

#1: DNA chain DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*G)-3')


Mass: 2468.617 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*GP*CP*GP*CP*C)-3')


Mass: 2099.387 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein DNA POLYMERASE BETA


Mass: 38388.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P06766

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Non-polymers , 3 types, 7 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: DPOB_RAT SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ARG 227 LEU A 228 ARG 227 LEU B 228 THE N-TERMINAL METHIONINE IS INCLUDED IN THE GENE SEQUENCE EVEN THOUGH IT IS REMOVED AFTER TRANSLATION IN THE CELL; SEE MATSUKAGE ET AL., J. BIOL. CHEM. 262, 8960, (1987). FOR THE AMINO ACID SEQUENCE, SEE A. KUMAR ET AL., J. BIOL. CHEM. 265, 2124, (1990).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growpH: 6.5 / Details: pH 6.50
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MES11
3MGCL211
4LI SULFATE11
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140-75 mMlithium sulfate1reservoir
210 mg/mlpol beta1drop
310 mM1dropMgCl2
41

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3.6 Å / Num. all: 25046 / Num. obs: 10650 / % possible obs: 96 %
Reflection
*PLUS
Highest resolution: 3.6 Å / % possible obs: 96 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 3.6→20 Å / σ(F): 0 / σ(I): 0 /
RfactorNum. reflection
obs0.199 10650
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5083 612 55 4 5754
Refinement
*PLUS
Highest resolution: 3.6 Å / Lowest resolution: 20 Å / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_d2.89

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