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- PDB-6i8a: The crystal structure of the Pol2 catalytic domain of DNA polymer... -

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Basic information

Entry
Database: PDB / ID: 6i8a
TitleThe crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution.
Components
  • DNA polymerase epsilon catalytic subunit A
  • Primer DNA
  • Template DNA
KeywordsDNA BINDING PROTEIN / DNA / Pol2 / P301R / P286R / cancer / endometrial / Pol epsilon
Function / homology
Function and homology information


gene conversion / DNA replication initiation / epsilon DNA polymerase complex / nucleotide-excision repair, DNA gap filling / SUMO binding / DNA replication proofreading / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling ...gene conversion / DNA replication initiation / epsilon DNA polymerase complex / nucleotide-excision repair, DNA gap filling / SUMO binding / DNA replication proofreading / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / mitotic sister chromatid cohesion / leading strand elongation / nuclear replication fork / error-prone translesion synthesis / base-excision repair, gap-filling / replication fork / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / double-strand break repair / single-stranded DNA binding / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / mRNA binding / DNA binding / zinc ion binding / nucleus
Similarity search - Function
DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / DNA polymerase family B, thumb domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily ...DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / DNA polymerase family B, thumb domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase epsilon catalytic subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.652 Å
AuthorsParkash, V. / Johansson, E.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation2011.0042 Sweden
CitationJournal: Nat Commun / Year: 2019
Title: Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon.
Authors: Parkash, V. / Kulkarni, Y. / Ter Beek, J. / Shcherbakova, P.V. / Kamerlin, S.C.L. / Johansson, E.
History
DepositionNov 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase epsilon catalytic subunit A
P: Primer DNA
T: Template DNA
B: DNA polymerase epsilon catalytic subunit A
C: Primer DNA
D: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,88814
Polymers290,6346
Non-polymers1,2548
Water1086
1
A: DNA polymerase epsilon catalytic subunit A
P: Primer DNA
T: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,9447
Polymers145,3173
Non-polymers6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-55 kcal/mol
Surface area49530 Å2
MethodPISA
2
B: DNA polymerase epsilon catalytic subunit A
C: Primer DNA
D: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,9447
Polymers145,3173
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-52 kcal/mol
Surface area49370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.466, 70.257, 159.335
Angle α, β, γ (deg.)90.000, 112.850, 90.000
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase epsilon catalytic subunit A / DNA polymerase II subunit A


Mass: 137134.562 Da / Num. of mol.: 2 / Mutation: P301R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: POL2, DUN2, YNL262W, N0825 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21951, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules PCTD

#2: DNA chain Primer DNA


Mass: 3293.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Template DNA


Mass: 4889.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 14 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50mM MES pH 6.5, 150mM NaAc, 8%PEG20K / PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 4, 2017
RadiationMonochromator: Si (111) Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→19.957 Å / Num. obs: 91152 / % possible obs: 98.7 % / Redundancy: 3.422 % / Biso Wilson estimate: 72.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.089 / Χ2: 1.026 / Net I/σ(I): 10.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.813.4541.2030.89140070.5691.42594.5
2.81-3.013.4840.6441.7142030.8090.76299.7
3.01-3.253.3750.3433.12128340.9430.40899.7
3.25-3.553.5150.1596.63115910.9890.18899.6
3.55-3.973.310.09311.35108350.9940.11199.4
3.97-4.583.5080.05219.1895570.9980.06299.6
4.58-5.63.360.0423.1981170.9980.04899.4
5.6-7.863.3450.03524.2163270.9990.04299.4
7.86-19.9573.30.0235.5336810.9990.02498.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m8o

4m8o


Resolution: 2.652→19.957 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.77
RfactorNum. reflection% reflection
Rfree0.2792 4564 5.04 %
Rwork0.2289 --
obs0.2315 90534 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.46 Å2 / Biso mean: 78.0084 Å2 / Biso min: 41.32 Å2
Refinement stepCycle: final / Resolution: 2.652→19.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16938 1055 66 6 18065
Biso mean--55.97 72.44 -
Num. residues----2251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6519-2.68190.41361150.39342290240579
2.6819-2.71340.46171420.38072821296397
2.7134-2.74640.37151710.36172805297699
2.7464-2.78110.3741540.3482880303499
2.7811-2.81760.4141520.348328953047100
2.8176-2.85610.37721480.34428422990100
2.8561-2.89680.39011630.316828963059100
2.8968-2.93990.34791420.318928743016100
2.9399-2.98570.36461550.309228362991100
2.9857-3.03440.31791450.31322914305999
3.0344-3.08660.37291590.30322849300899
3.0866-3.14250.31581480.292728823030100
3.1425-3.20270.30851320.29072903303599
3.2027-3.26780.38961430.28872880302399
3.2678-3.33850.3221650.279429093074100
3.3385-3.41580.2991400.253228302970100
3.4158-3.50080.29871610.24612881304299
3.5008-3.59490.29371580.241128733031100
3.5949-3.70010.30571630.24642892305599
3.7001-3.81870.31141370.24842862299999
3.8187-3.95420.30591440.22952919306399
3.9542-4.11120.25241550.220228693024100
4.1112-4.29650.25411430.204329093052100
4.2965-4.52050.25421640.190328773041100
4.5205-4.80010.25071430.187129413084100
4.8001-5.16470.23311480.195729153063100
5.1647-5.67360.25691570.192929243081100
5.6736-6.470.29311690.210229393108100
6.47-8.06110.24651730.19712920309399
8.0611-19.95770.18931750.16052943311897

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