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- PDB-3u7e: Crystal structure of mPNKP catalytic fragment (D170A) -

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Basic information

Entry
Database: PDB / ID: 3u7e
TitleCrystal structure of mPNKP catalytic fragment (D170A)
ComponentsBifunctional polynucleotide phosphatase/kinase
KeywordsHYDROLASE / TRANSFERASE / protein-DNA complex / HAD family / pnkp / DNA repair / phosphatase
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 / protein K63-linked ubiquitination / ubiquitin-like ligase-substrate adaptor activity / double-strand break repair via nonhomologous end joining ...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 / protein K63-linked ubiquitination / ubiquitin-like ligase-substrate adaptor activity / double-strand break repair via nonhomologous end joining / site of double-strand break / double-stranded DNA binding / DNA repair / DNA damage response / 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 / SMAD/FHA domain superfamily / HAD superfamily/HAD-like ...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 / SMAD/FHA domain superfamily / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Bifunctional polynucleotide phosphatase/kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCoquelle, N. / Havali, Z. / Bernstein, N. / Green, R. / Glover, J.N.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates.
Authors: Coquelle, N. / Havali-Shahriari, Z. / Bernstein, N. / Green, R. / Glover, J.N.
#1: Journal: 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
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name / _software.name
Revision 1.3Sep 13, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Bifunctional polynucleotide phosphatase/kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9588
Polymers42,3791
Non-polymers5807
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.820, 63.190, 68.120
Angle α, β, γ (deg.)90.000, 88.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bifunctional polynucleotide phosphatase/kinase / DNA 5'-kinase/3'-phosphatase / Polynucleotide kinase-3'-phosphatase / Polynucleotide 3'-phosphatase ...DNA 5'-kinase/3'-phosphatase / Polynucleotide kinase-3'-phosphatase / Polynucleotide 3'-phosphatase / 2'(3')-polynucleotidase / Polynucleotide 5'-hydroxyl-kinase


Mass: 42378.699 Da / Num. of mol.: 1 / Mutation: D170A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pnkp / Plasmid: pet19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9JLV6, polynucleotide 3'-phosphatase, polynucleotide 5'-hydroxyl-kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, pH 7, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→46.3 Å / Num. all: 40013 / Num. obs: 40013 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.108 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.750.5342.78124633316199.8
1.75-1.80.4423.26110682948199.9
1.8-1.90.3214.42189035018199.9
1.9-20.2146.6152914062199.8
2-2.50.10911.864532711973199.9
2.5-30.05719.93201085302199.8
3-60.03332.08243126442199.8
6-100.02835.422735740199.9
10-46.30.02538.5716212196.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YJ5

1yj5


Resolution: 1.7→46.3 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8917 / SU ML: 0.39 / σ(F): -3 / Phase error: 18.21 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1999 5 %RANDOM
Rwork0.161 ---
all0.1627 39992 --
obs0.1627 39992 99.83 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.26 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 106.07 Å2 / Biso mean: 25.227 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.2355 Å20 Å2-0.7397 Å2
2--3.7886 Å2-0 Å2
3----2.5531 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 36 451 3420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093124
X-RAY DIFFRACTIONf_angle_d1.164250
X-RAY DIFFRACTIONf_chiral_restr0.069460
X-RAY DIFFRACTIONf_plane_restr0.007554
X-RAY DIFFRACTIONf_dihedral_angle_d13.8271171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7001-1.74260.25831420.216326892831
1.7426-1.78970.23811430.196327222865
1.7897-1.84240.21931420.181327042846
1.8424-1.90190.24191410.185626792820
1.9019-1.96980.19751420.172326882830
1.9698-2.04870.19331430.159627202863
2.0487-2.14190.19391420.156827072849
2.1419-2.25490.22891430.15427112854
2.2549-2.39610.19041430.154827072850
2.3961-2.58110.2021420.15926972839
2.5811-2.84090.20771440.167627352879
2.8409-3.25180.19851410.156527122853
3.2518-4.09660.15551440.145427332877
4.0966-46.3340.18281470.156427892936
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)
10.81210.29520.31710.68510.01811.11790.0224-0.08330.06560.05150.00370.0542-0.0656-0.0293-0.00170.0832-0.00210.0080.04940.00630.078417.933815.692114.851
20.33220.0994-0.20080.4221-0.12740.30970.0328-0.0521-0.0094-0.0137-0.05310.2178-0.1869-0.2290.0040.14960.03510.00080.0913-0.03250.129710.777823.841612.9381
30.8398-0.42320.60981.17290.48431.2590.0021-0.0416-0.07790.0498-0.00510.12470.062-0.0629-0.00540.0875-0.00450.01170.05050.00490.093715.517910.4854.942
40.6045-0.11690.47410.0990.16441.37110.1135-0.0484-0.60150.05440.02980.33740.701-0.260.14350.1557-0.0642-0.0264-0.21750.06350.213612.6388-0.41498.1937
50.0409-0.01720.2215-0.0207-0.02580.85470.04750.089-0.06340.05030.063-0.11290.08740.360.03880.14390.0226-0.02710.2041-0.00580.1513-0.5017.7145-28.1488
60.76650.36170.75910.2420.16771.2199-0.1141-0.28770.26730.0316-0.0130.0893-0.2534-0.4488-0.07530.14360.0338-00.1861-0.00880.1338-10.121814.3559-26.7764
70.9644-0.2568-0.08110.5711-0.21890.18160.1138-0.21950.30750.076-0.1454-0.0924-0.126-0.4856-0.04380.1101-0.01070.04690.40910.02350.133-6.13314.7392-11.1354
80.2838-0.1010.28660.27230.1540.48480.10840.2123-0.1643-0.04190.114-0.07960.23070.07210.03190.1339-0.03140.00390.2018-0.00210.14162.44846.3883-19.8141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain B and (resseq 142:217)B142 - 217
2X-RAY DIFFRACTION2chain B and (resseq 218:242)B218 - 242
3X-RAY DIFFRACTION3chain B and (resseq 243:316)B243 - 316
4X-RAY DIFFRACTION4chain B and (resseq 317:341)B317 - 341
5X-RAY DIFFRACTION5chain B and (resseq 342:384)B342 - 384
6X-RAY DIFFRACTION6chain B and (resseq 385:466)B385 - 466
7X-RAY DIFFRACTION7chain B and (resseq 467:484)B467 - 484
8X-RAY DIFFRACTION8chain B and (resseq 485:522)B485 - 522

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