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- PDB-3pzp: Human DNA polymerase kappa extending opposite a cis-syn thymine dimer -

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Basic information

Entry
Database: PDB / ID: 3pzp
TitleHuman DNA polymerase kappa extending opposite a cis-syn thymine dimer
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3'
  • 5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
  • DNA polymerase kappa
KeywordsTRANSFERASE/DNA / DNA Nucleotidyltransferase / DNA Binding Nucleotide Binding Magnesium Binding / Nucleus / 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 / nucleus / metal ion binding / cytosol
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'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase kappa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.336 Å
AuthorsVasquez-Del Carpio, R. / Silverstein, T.D. / Lone, S. / Johnson, R.E. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Role of human DNA polymerase kappa in extension opposite from a cis-syn thymine dimer.
Authors: Vasquez-Del Carpio, R. / Silverstein, T.D. / Lone, S. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_ref_seq_dif.details / _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
A: DNA polymerase kappa
B: DNA polymerase kappa
P: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3'
T: 5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
Q: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3'
U: 5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,75412
Polymers136,6756
Non-polymers1,0806
Water1448
1
A: DNA polymerase kappa
P: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3'
T: 5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8776
Polymers68,3373
Non-polymers5403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-48 kcal/mol
Surface area25900 Å2
MethodPISA
2
B: DNA polymerase kappa
Q: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3'
U: 5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8776
Polymers68,3373
Non-polymers5403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-49 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.136, 154.476, 217.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 58901.195 Da / Num. of mol.: 2 / Fragment: Residues 19-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLK, DINB1 / Plasmid: pBJ943 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5464 / References: UniProt: Q9UBT6, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules PQTU

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


Mass: 4090.673 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Oligonucleotide
#3: DNA chain 5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'


Mass: 5345.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Oligonucleotide

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Non-polymers , 3 types, 14 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.61 Å3/Da / Density % sol: 65.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 5000 monomethylether, 0.2M potassium acetate, 0.1M sodium chloride, 0.1M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 22, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. all: 31785 / Num. obs: 31594 / % possible obs: 99.4 % / Redundancy: 4.8 % / Rsym value: 0.112 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rsym valueDiffraction-ID% possible all
3.23-3.354.20.866195.3
3.35-3.484.70.728199.4
3.48-3.644.90.5411100
3.64-3.8350.381100
3.83-4.0750.2471100
4.07-4.384.90.1571100
4.38-4.824.90.1081100
4.82-5.524.90.0991100
5.52-6.954.80.0811100
6.95-504.60.025199.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OH2

2oh2


Resolution: 3.336→46.67 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 1 / SU B: 51.341 / SU ML: 0.478 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28778 1452 5 %RANDOM
Rwork0.24165 ---
obs0.24389 27432 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.177 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--8.43 Å20 Å2
3----9.24 Å2
Refinement stepCycle: LAST / Resolution: 3.336→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 1127 64 8 7743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0217974
X-RAY DIFFRACTIONr_bond_other_d0.0020.024821
X-RAY DIFFRACTIONr_angle_refined_deg1.6812.15211072
X-RAY DIFFRACTIONr_angle_other_deg0.976311881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60425.199277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.574151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4091532
X-RAY DIFFRACTIONr_chiral_restr0.0940.21287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021381
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3031.54404
X-RAY DIFFRACTIONr_mcbond_other0.041.51771
X-RAY DIFFRACTIONr_mcangle_it0.58326992
X-RAY DIFFRACTIONr_scbond_it0.933570
X-RAY DIFFRACTIONr_scangle_it1.644.54072
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.336→3.422 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 115 -
Rwork0.339 1826 -
obs--92.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.7051-1.4282-6.36491.8654-0.43617.33320.65260.76460.47130.3113-0.1469-0.0552-1.2439-1.4305-0.50570.98390.2884-0.02250.9649-0.16250.416933.792838.842969.6666
22.4559-0.2508-0.93534.9396-2.07575.6306-0.05730.3082-0.37470.44490.00931.0132-0.0516-2.04850.0480.254-0.07390.1951.0894-0.16790.521823.286322.597781.5891
34.93091.8018-3.34773.4855-0.75289.7983-0.51880.3746-0.82220.3267-0.2004-0.11731.7461-0.47750.71910.6812-0.2310.18740.1-0.09610.435744.5033.300974.9567
45.2174-0.1441-0.704910.86513.947111.6365-0.05050.002-0.05070.495-0.1847-0.4832-0.17460.6140.23520.039-0.02060.00680.02290.04930.132655.68623.54263.1216
52.04140.3473-1.11993.5714-1.39787.1337-0.08821.3808-0.3739-0.83860.13170.39320.4813-2.4645-0.04350.28160.1541-0.06041.7441-0.19620.468431.79523.912644.5672
63.6656-0.5032-0.15070.7391.56553.8521-0.992-0.11220.2078-0.23151.3196-0.2603-0.11761.1172-0.32761.07060.2850.31841.3748-0.00470.725737.110519.4435114.7321
72.2745-1.9782-0.78063.9975-0.68013.9093-0.63970.2847-0.53020.22980.36110.77430.063-1.16210.27860.4899-0.0440.25820.7758-0.08540.522521.830221.6085100.8496
87.34360.02631.20893.31274.817912.6783-0.1548-0.13150.99440.159-0.01630.2979-1.1963-1.10640.17110.99880.47630.14840.60750.03770.685216.554148.7449108.1961
94.8152-1.41933.50320.35152.077218.8318-0.2887-0.55570.6622-0.35980.3153-0.638-1.64720.7624-0.02660.89470.24720.15341.0609-0.11360.93736.533844.0157124.0349
104.8499-0.1472-4.02811.92150.71049.446-0.9323-1.3145-0.85990.29390.1210.38361.97970.79840.81131.02390.560.37030.73430.11750.608318.315324.0588137.8269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 78
2X-RAY DIFFRACTION2A79 - 100
3X-RAY DIFFRACTION2A339 - 401
4X-RAY DIFFRACTION3A101 - 109
5X-RAY DIFFRACTION3A171 - 338
6X-RAY DIFFRACTION4A110 - 170
7X-RAY DIFFRACTION5A402 - 518
8X-RAY DIFFRACTION6B20 - 78
9X-RAY DIFFRACTION7B79 - 100
10X-RAY DIFFRACTION7B339 - 401
11X-RAY DIFFRACTION8B101 - 109
12X-RAY DIFFRACTION8B171 - 338
13X-RAY DIFFRACTION9B110 - 170
14X-RAY DIFFRACTION10B402 - 518

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