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- PDB-2w3o: Crystal structure of the human PNKP FHA domain in complex with an... -

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Basic information

Entry
Database: PDB / ID: 2w3o
TitleCrystal structure of the human PNKP FHA domain in complex with an XRCC1-derived phosphopeptide
Components
  • BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
  • DNA REPAIR PROTEIN XRCC1
KeywordsHYDROLASE / TRANSFERASE/PEPTIDE / FHA / PNKP / XRCC1 / KINASE / NUCLEUS / POLYNUCLEOTIDE KINASE 3' PHOSPHATASE / DNA DAMAGE / DNA REPAIR / TRANSFERASE / ATP-BINDING / MULTIFUNCTIONAL ENZYME / POLYMORPHISM / PHOSPHOPROTEIN / PHOSPHO- PEPTIDE / NUCLEOTIDE-BINDING / BASE EXCISION REPAIR / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


purine nucleotide binding / polynucleotide 3'-phosphatase / 3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / polynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity ...purine nucleotide binding / polynucleotide 3'-phosphatase / 3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / polynucleotide 3'-phosphatase activity / polynucleotide 5'-hydroxyl-kinase / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / regulation of base-excision repair / single strand break repair / HDR through MMEJ (alt-NHEJ) / response to hydroperoxide / Resolution of AP sites via the single-nucleotide replacement pathway / positive regulation of double-strand break repair via nonhomologous end joining / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / positive regulation of telomere maintenance / site of DNA damage / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / nucleotide-excision repair / hippocampus development / response to radiation / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / site of double-strand break / response to oxidative stress / double-stranded DNA binding / endonuclease activity / damaged DNA binding / chromosome, telomeric region / DNA repair / chromatin / nucleolus / enzyme binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
Bifunctional polynucleotide phosphatase/kinase PNKP / Polynucleotide 3'-phosphatase / Polynucleotide kinase 3 phosphatase / Polynucleotide kinase 3 phosphatase / DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / PNK, FHA domain / FHA domain / HAD-superfamily hydrolase,subfamily IIIA ...Bifunctional polynucleotide phosphatase/kinase PNKP / Polynucleotide 3'-phosphatase / Polynucleotide kinase 3 phosphatase / Polynucleotide kinase 3 phosphatase / DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / PNK, FHA domain / FHA domain / HAD-superfamily hydrolase,subfamily IIIA / AAA domain / Tumour Suppressor Smad4 - #20 / BRCT domain / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / HAD superfamily / HAD-like superfamily / Galactose-binding-like domain superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
DNA repair protein XRCC1 / Bifunctional polynucleotide phosphatase/kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOliver, A.W. / Ali, A.A.E. / Pearl, L.H.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Specific Recognition of a Multiply Phosphorylated Motif in the DNA Repair Scaffold Xrcc1 by the Fha Domain of Human Pnk.
Authors: Ali, A.A.E. / Jukes, R.M. / Pearl, L.H. / Oliver, A.W.
History
DepositionNov 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_conn_type
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_alt_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.ptnr1_symmetry / _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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: DNA REPAIR PROTEIN XRCC1
D: DNA REPAIR PROTEIN XRCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,50710
Polymers26,2674
Non-polymers2406
Water5,152286
1
A: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
C: DNA REPAIR PROTEIN XRCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2545
Polymers13,1332
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-4.9 kcal/mol
Surface area7130 Å2
MethodPQS
2
B: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
D: DNA REPAIR PROTEIN XRCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2545
Polymers13,1332
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-3.6 kcal/mol
Surface area7210 Å2
MethodPQS
Unit cell
Length a, b, c (Å)56.900, 56.900, 62.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

21B-2011-

HOH

31B-2051-

HOH

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Components

#1: Protein BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE / FHA DOMAIN OF POLYNUCLEOTIDE KINASE 3' PHOSPHATASE / DNA 5'-KINASE/3'-PHOSPHATASE / POLYNUCLEOTIDE ...FHA DOMAIN OF POLYNUCLEOTIDE KINASE 3' PHOSPHATASE / DNA 5'-KINASE/3'-PHOSPHATASE / POLYNUCLEOTIDE 5'-HYDROXYL-KINASE / POLYNUCLEOTIDE 3'-PHOSPHATASE


Mass: 12117.620 Da / Num. of mol.: 2 / Fragment: FHA DOMAIN, RESIDUES 1-110 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Plasmid: PTWO-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS
References: UniProt: Q96T60, polynucleotide 3'-phosphatase, polynucleotide 5'-hydroxyl-kinase
#2: Protein/peptide DNA REPAIR PROTEIN XRCC1 / X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 1 / XRCC1-DERIVED PHOSPHOPEPTIDE


Mass: 1015.764 Da / Num. of mol.: 2 / Fragment: RESIDUES 515-522 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P18887
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 99 TO GLU ENGINEERED RESIDUE IN CHAIN B, LEU 99 TO GLU
Has protein modificationY
Sequence detailsTHE SEQUENCE THAT WAS SYNTHESIZED WAS TAKEN FROM THAT REPORTED IN "MOLECULAR CLONING OF THE HUMAN ...THE SEQUENCE THAT WAS SYNTHESIZED WAS TAKEN FROM THAT REPORTED IN "MOLECULAR CLONING OF THE HUMAN GENE, PNKP, ENCODING A POLYNUCLEOTID KINASE 3'-PHOSPHATASE AND EVIDENCE FOR ITS ROLE IN REPAIR OF DNA STRAND BREAKS CAUSED BY OXIDATIVE DAMAGE." JILANI A., RAMOTAR D., SLACK C., ONG C., YANG X.M., SCHERER S.W., LASKO D.D. J. BIOL. CHEM. 274:24176-24186(1999), WHICH HAS A GLYCINE AT POSITION 18 INSTEAD OF A GLUTAMIC ACID.

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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: 2.63 Å3/Da / Density % sol: 53.33 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL PH 8.5, 0.25 M CACL2, 28% W/V PEG 4000, 0.2 M NDSB-221

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.208
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2008 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.208 Å / Relative weight: 1
ReflectionResolution: 1.85→38.75 Å / Num. obs: 19211 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.37 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.78
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.12 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.43 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BRF

2brf


Resolution: 1.85→62.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.452 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 977 5.1 %RANDOM
Rwork0.178 ---
obs0.181 18234 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å2-0 Å2
2---0.29 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.85→62.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 6 286 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.722.0222328
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06124.70668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63515.228263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5911512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221266
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0521.51087
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81721760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6593605
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3494.5564
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 65
Rwork0.273 1271

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