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- PDB-3zvm: The structural basis for substrate recognition by mammalian polyn... -

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Basic information

Entry
Database: PDB / ID: 3zvm
TitleThe structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase
Components
  • 5'-D(*GP*TP*CP*AP*CP)-3'
  • BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
KeywordsHYDROLASE/TRANSFERASE/DNA / HYDROLASE-TRANSFERASE-DNA COMPLEX / BASE EXCISION REPAIR / BER / NON-HOMOLOGOUS END-JOINING / NHEJ / DNA REPAIR / CANCER
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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / DNA / Bifunctional polynucleotide phosphatase/kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsGarces, F. / Pearl, L.H. / Oliver, A.W.
CitationJournal: Mol. Cell / Year: 2011
Title: The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase.
Authors: Garces, F. / Pearl, L.H. / Oliver, A.W.
History
DepositionJul 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen / pdbx_entity_src_syn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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.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_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: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
B: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
E: 5'-D(*GP*TP*CP*AP*CP)-3'
F: 5'-D(*GP*TP*CP*AP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,10822
Polymers94,8244
Non-polymers2,28318
Water21,5461196
1
B: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
F: 5'-D(*GP*TP*CP*AP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,61312
Polymers47,4122
Non-polymers1,20110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
E: 5'-D(*GP*TP*CP*AP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,49510
Polymers47,4122
Non-polymers1,0828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.817, 75.243, 135.199
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain , 2 types, 4 molecules ABEF

#1: Protein BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE / DNA 5'-KINASE/3'-PHOSPHATASE / POLYNUCLEOTIDE KINASE-3'-PHOSPHATASE / PNKP


Mass: 45932.227 Da / Num. of mol.: 2
Fragment: POLYNUCLEOTIDE 3'-PHOSPHATASE AND POLYNUCLEOTIDE 5'-HYDROXYL-KINASE DOMAINS, RESIDUES 111-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 PLYSS
References: UniProt: Q9JLV6, polynucleotide 3'-phosphatase, polynucleotide 5'-hydroxyl-kinase
#2: DNA chain 5'-D(*GP*TP*CP*AP*CP)-3'


Mass: 1480.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 1214 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1196 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7.0, 18% (W/V) PEG 12000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: BRUKER / Detector: CCD / Date: Feb 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→38.5 Å / Num. obs: 60655 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.12 % / Biso Wilson estimate: 15.22 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.32
Reflection shellResolution: 2→2.04 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PROTEUM2data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YJ5

1yj5


Resolution: 1.997→38.49 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 17.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 3071 5.1 %
Rwork0.152 --
obs0.1545 60655 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.72 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3145 Å20 Å2-0.1286 Å2
2---0.3667 Å20 Å2
3---0.0522 Å2
Refinement stepCycle: LAST / Resolution: 1.997→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5920 116 144 1196 7376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076402
X-RAY DIFFRACTIONf_angle_d1.0998718
X-RAY DIFFRACTIONf_dihedral_angle_d17.6382395
X-RAY DIFFRACTIONf_chiral_restr0.067936
X-RAY DIFFRACTIONf_plane_restr0.0051111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9971-2.06840.24493010.1695618X-RAY DIFFRACTION98
2.0684-2.15130.21793030.16545782X-RAY DIFFRACTION100
2.1513-2.24920.23512880.16335753X-RAY DIFFRACTION100
2.2492-2.36770.21742860.15385786X-RAY DIFFRACTION100
2.3677-2.5160.2092990.15885707X-RAY DIFFRACTION100
2.516-2.71030.20472980.1535760X-RAY DIFFRACTION100
2.7103-2.98290.21223120.15695763X-RAY DIFFRACTION100
2.9829-3.41430.21733300.14525780X-RAY DIFFRACTION100
3.4143-4.30080.16113480.12875729X-RAY DIFFRACTION100
4.3008-38.49670.17093060.15045906X-RAY DIFFRACTION100

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