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- PDB-4u6p: Structural mechanism of error-free bypass of major benzo[a]pyrene... -

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Basic information

Entry
Database: PDB / ID: 4u6p
TitleStructural mechanism of error-free bypass of major benzo[a]pyrene adduct by human polymerase kappa
Components
  • DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*AP*TP*CP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3')
  • DNA polymerase kappaPOLK
KeywordsTRANSFERASE/DNA / benzo[a]pyrene-N2-Guanine / DNA replication / DNA damage tolerance / polymerase kappa / Environment pollution / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV ...nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I ...DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / DNA polymerase kappa
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.593 Å
AuthorsJha, V.K. / Ling, H.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase kappa.
Authors: Jha, V. / Bian, C. / Xing, G. / Ling, H.
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Derived calculations
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Jun 15, 2016Group: Database references
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase kappa
B: DNA polymerase kappa
C: DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3')
D: DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*AP*TP*CP*CP*GP*C)-3')
P: DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3')
T: DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*AP*TP*CP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,01515
Polymers133,8166
Non-polymers1,1989
Water1,856103
1
A: DNA polymerase kappa
C: DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3')
D: DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*AP*TP*CP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4327
Polymers66,9083
Non-polymers5244
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-39 kcal/mol
Surface area24570 Å2
MethodPISA
2
B: DNA polymerase kappa
P: DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3')
T: DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*AP*TP*CP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5828
Polymers66,9083
Non-polymers6745
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-37 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.150, 129.286, 167.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase kappa / POLK / DINB protein / DINP


Mass: 60184.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLK, DINB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pRARE / References: UniProt: Q9UBT6, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules CPDT

#2: DNA chain DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3')


Mass: 2740.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*AP*TP*CP*CP*GP*C)-3')


Mass: 3982.596 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Non-polymers , 4 types, 112 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: isolated from a natural source / 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: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: PEG 400 and potassium acetate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.48→46.233 Å / Num. obs: 50663 / % possible obs: 96.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.2 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OH2

2oh2


Resolution: 2.593→46.233 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1066 2.4 %
Rwork0.2002 --
obs0.2011 44341 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.593→46.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 894 70 103 7767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087870
X-RAY DIFFRACTIONf_angle_d1.1810808
X-RAY DIFFRACTIONf_dihedral_angle_d19.1623025
X-RAY DIFFRACTIONf_chiral_restr0.0471238
X-RAY DIFFRACTIONf_plane_restr0.0061222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5932-2.71120.39721190.32275183X-RAY DIFFRACTION95
2.7112-2.85410.31951420.28555435X-RAY DIFFRACTION100
2.8541-3.03290.35411340.26855441X-RAY DIFFRACTION99
3.0329-3.2670.25561300.23855423X-RAY DIFFRACTION99
3.267-3.59560.23861470.20325437X-RAY DIFFRACTION99
3.5956-4.11560.25241330.18915454X-RAY DIFFRACTION98
4.1156-5.18420.18521390.16475433X-RAY DIFFRACTION97
5.1842-46.24040.20861220.17775469X-RAY DIFFRACTION94

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