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- PDB-1yj5: Molecular architecture of mammalian polynucleotide kinase, a DNA ... -

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Basic information

Entry
Database: PDB / ID: 1yj5
TitleMolecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme
Components
  • 5' polynucleotide kinase-3' phosphatase FHA domain
  • 5' polynucleotide kinase-3' phosphatase catalytic domain
KeywordsTRANSFERASE / Beta sandwich / P-loop
Function / homology
Function and homology information


polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping ...polynucleotide 3'-phosphatase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase activity / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA ligation involved in DNA repair / SCF ubiquitin ligase complex / positive regulation of double-strand break repair via nonhomologous end joining / protein K63-linked ubiquitination / positive regulation of telomere capping / ubiquitin-like ligase-substrate adaptor activity / positive regulation of telomere maintenance via telomerase / double-strand break repair via nonhomologous end joining / site of double-strand break / double-stranded DNA binding / response to oxidative stress / phosphorylation / DNA repair / DNA damage response / nucleolus / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Bifunctional polynucleotide phosphatase/kinase PNKP / Polynucleotide 3'-phosphatase / Polynucleotide kinase 3 phosphatase / Polynucleotide kinase 3 phosphatase / PNK, FHA domain / FHA domain / HAD-superfamily hydrolase,subfamily IIIA / AAA domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 ...Bifunctional polynucleotide phosphatase/kinase PNKP / Polynucleotide 3'-phosphatase / Polynucleotide kinase 3 phosphatase / Polynucleotide kinase 3 phosphatase / PNK, FHA domain / FHA domain / HAD-superfamily hydrolase,subfamily IIIA / AAA domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / P-loop containing nucleotide triphosphate hydrolases / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Bifunctional polynucleotide phosphatase/kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsBernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. ...Bernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. / Durocher, D. / Weinfeld, M. / Glover, J.N.M.
CitationJournal: Mol.Cell / Year: 2005
Title: The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.
Authors: Bernstein, N.K. / Williams, R.S. / Rakovszky, M.L. / Cui, D. / Green, R. / Karimi-Busheri, F. / Mani, R.S. / Galicia, S. / Koch, C.A. / Cass, C.E. / Durocher, D. / Weinfeld, M. / Glover, J.N.
History
DepositionJan 13, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5' polynucleotide kinase-3' phosphatase catalytic domain
B: 5' polynucleotide kinase-3' phosphatase catalytic domain
C: 5' polynucleotide kinase-3' phosphatase FHA domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,84915
Polymers100,6963
Non-polymers1,15312
Water1,40578
1
A: 5' polynucleotide kinase-3' phosphatase catalytic domain
B: 5' polynucleotide kinase-3' phosphatase catalytic domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,53914
Polymers85,3862
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-212 kcal/mol
Surface area36030 Å2
MethodPISA
2
C: 5' polynucleotide kinase-3' phosphatase FHA domain


Theoretical massNumber of molelcules
Total (without water)15,3101
Polymers15,3101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.473, 169.872, 77.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer.

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Components

#1: Protein 5' polynucleotide kinase-3' phosphatase catalytic domain / polynucleotide kinase


Mass: 42693.082 Da / Num. of mol.: 2 / Fragment: residues 140-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold 99
References: UniProt: Q9JLV6, polynucleotide 5'-hydroxyl-kinase
#2: Protein 5' polynucleotide kinase-3' phosphatase FHA domain / polynucleotide kinase


Mass: 15310.164 Da / Num. of mol.: 1 / Fragment: residues 1-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold 99
References: UniProt: Q9JLV6, polynucleotide 5'-hydroxyl-kinase
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.8 Å3/Da / Density % sol: 31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1M Tris (pH 8.3 - 8.7), 18-20% PEG 5000 MME, 0.1M Li2SO4, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0199, 0.9793, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 20, 2003
RadiationMonochromator: mirror, Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.01991
20.97931
30.97971
ReflectionResolution: 2.8→30 Å / Num. obs: 31529 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.095 / Net I/σ(I): 13.1
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.448 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→29.75 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.877 / SU B: 29.81 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.033 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 1562 5 %RANDOM
Rwork0.21856 ---
obs0.22029 29868 99.54 %-
all-31529 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.374 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å20 Å2
2--5.27 Å20 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 60 78 6844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226926
X-RAY DIFFRACTIONr_angle_refined_deg0.9231.9779418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8185864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01223.345296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.691552
X-RAY DIFFRACTIONr_chiral_restr0.0590.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025294
X-RAY DIFFRACTIONr_nbd_refined0.1430.32915
X-RAY DIFFRACTIONr_nbtor_refined0.3050.54599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.5325
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0890.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.58
X-RAY DIFFRACTIONr_mcbond_it0.2011.54429
X-RAY DIFFRACTIONr_mcangle_it0.36126983
X-RAY DIFFRACTIONr_scbond_it0.47832790
X-RAY DIFFRACTIONr_scangle_it0.7724.52435
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 96 -
Rwork0.307 2113 -
obs--96.04 %
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)
10.9971-0.68210.83441.3413-1.05451.5185-0.0101-0.0174-0.0221-0.0307-0.0022-0.00470.06730.03270.01230.0662-0.03340.02220.02-0.01180.133343.20739.54577.658
20.9132-0.48741.04381.0855-1.21842.7110.0670.1705-0.2171-0.01930.03410.03760.13130.0194-0.10110.0328-0.00870.01260.0531-0.07780.168223.97335.50937.435
30.92572.3296-0.720211.71820.7127.9751-0.2852-0.35730.1245-1.00260.3805-0.27390.26260.3332-0.09530.24340.127-0.00760.24750.08150.301657.9057.53745.334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA144 - 5225 - 383
2X-RAY DIFFRACTION2BB140 - 5221 - 383
3X-RAY DIFFRACTION3CC6 - 1106 - 110

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