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- PDB-1bpb: CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMM... -

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Entry
Database: PDB / ID: 1bpb
TitleCRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM
ComponentsDNA POLYMERASE BETA
KeywordsNUCLEOTIDYLTRANSFERASE
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 / damaged DNA binding / microtubule / 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 / Resolution: 2.3 Å
AuthorsSawaya, M.R. / Pelletier, H. / Kumar, A. / Wilson, S.H. / Kraut, J.
Citation
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.
#1: 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. / Wilson, S.H. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Studies of the Domain Structure of Mammalian DNA Polymerase Beta. Identification of a Discrete Template Binding Domain
Authors: Kumar, A. / Widen, S.G. / Williams, K.R. / Kedar, P. / Karpel, R.L. / Wilson, S.H.
History
DepositionApr 12, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.576, 63.520, 38.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: GLY 274 - SER 275 OMEGA =359.35 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

21A-477-

HOH

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Components

#1: Protein DNA POLYMERASE BETA


Mass: 28774.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P06766, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDNA POLYMERASE BETA POSSESSES A PROTEOLYTICALLY SENSITIVE REGION IN ITS AMINO ACID SEQUENCE ...DNA POLYMERASE BETA POSSESSES A PROTEOLYTICALLY SENSITIVE REGION IN ITS AMINO ACID SEQUENCE (RESIDUES 80 - 90), AND THE PRECISE CLEAVAGE SITE VARIES DEPENDING ON THE PROTEASE OR THE CHEMICAL REAGENT USED IN THE CLEAVAGE REACTION (SEE A. KUMAR ET AL., J. BIOL. CHEM. 265, 2124 (1990)). THE AUTHORS SUSPECT THAT A BACTERIAL PROTEASE OF UNKNOWN ORIGIN UNEXPECTEDLY CLEAVED THEIR INTACT ENZYME DURING THE CRYSTALLIZATION PROCESS, RESULTING IN CRYSTALS OF THE PROTEIN STRUCTURE REPORTED IN THIS ENTRY - THE 31-KD COOH-TERMINAL DOMAIN (RESIDUES 88 - 335) OF DNA POLYMERASE BETA. BECAUSE THE AUTHORS HAVE NOT DONE AN N-TERMINAL ANALYSIS ON THE PROTEIN IN THEIR CRYSTALS, THEIR CHOICE OF THE CLEAVAGE SITE (BETWEEN RESIDUES 87 AND 88) IS RATHER ARBITRARY, AND IN FACT, THERE MAY EVEN BE VARIABLE N-TERMINAL RESIDUES WITHIN ANY GIVEN CRYSTAL OF THIS CLEAVED PROTEIN. PLEASE NOTE THAT THIS ENTRY IS ONLY THE 31 KD DOMAIN AND THE FIRST 8 KD DOMAIN IS NOT PRESENT IN THIS STRUCTURE. PDB ADVISORY NOTICE: WATER MOLECULES 441, 468, AND 477 ARE VERY CLOSE TO SPECIAL POSITIONS.
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 228 THE PAPER BY KUMAR, ET AL., J.BIOL.CHEM., 265, 2124, (1990) REPORTS A CORRECTION TO THE SEQUENCE GIVEN IN SWISS-PROT (SEE REFERENCE 3 ABOVE).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 %(w/v)PEG33501drop
2100 mMTris1drop
315 mM1dropSrCl2
415 mg/ml39-kD pol beta1drop
5100 mMHEPES1drop
610 mM1drop(NH4)2SO4
725 %PEG33501reservoir
8100 mMHEPES1reservoir
915 mM1reservoirSrCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 13634 / Num. measured all: 33939 / Rmerge(I) obs: 0.045

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Processing

SoftwareName: TNT / Classification: refinement
RefinementHighest resolution: 2.3 Å / σ(F): 0 /
RfactorNum. reflection
obs0.193 13634
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 0 90 2024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.023
X-RAY DIFFRACTIONt_angle_deg3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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