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- PDB-6tx3: HPF1 bound to catalytic fragment of PARP2 -

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Basic information

Entry
Database: PDB / ID: 6tx3
TitleHPF1 bound to catalytic fragment of PARP2
Components
  • Histone PARylation factor 1
  • Poly [ADP-ribose] polymerase 2,Poly [ADP-ribose] polymerase 2
KeywordsTRANSFERASE / PARP2 / ARTD2 / ADP-ribosylation / serine ADP-ribosylation / HPF1 / C4orf27
Function / homology
Function and homology information


protein ADP-ribosyltransferase-substrate adaptor activity / regulation of protein ADP-ribosylation / response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity ...protein ADP-ribosyltransferase-substrate adaptor activity / regulation of protein ADP-ribosylation / response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding / HDR through MMEJ (alt-NHEJ) / DNA repair-dependent chromatin remodeling / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / extrinsic apoptotic signaling pathway / nucleosome binding / nucleotidyltransferase activity / DNA Damage Recognition in GG-NER / base-excision repair / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / histone binding / damaged DNA binding / DNA repair / DNA damage response / chromatin binding / chromatin / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Histone PARylation factor 1 / Histone PARylation factor 1 / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain ...Histone PARylation factor 1 / Histone PARylation factor 1 / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-UHB / Histone PARylation factor 1 / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsSuskiewicz, M.J. / Ahel, I.
Funding support United Kingdom, European Union, 5items
OrganizationGrant numberCountry
Wellcome Trust101794 United Kingdom
Wellcome Trust210634 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)B/R007195/1 United Kingdom
Cancer Research UKC35050/A22284 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 879-2017European Union
CitationJournal: Nature / Year: 2020
Title: HPF1 completes the PARP active site for DNA damage-induced ADP-ribosylation.
Authors: Suskiewicz, M.J. / Zobel, F. / Ogden, T.E.H. / Fontana, P. / Ariza, A. / Yang, J.C. / Zhu, K. / Bracken, L. / Hawthorne, W.J. / Ahel, D. / Neuhaus, D. / Ahel, I.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Poly [ADP-ribose] polymerase 2,Poly [ADP-ribose] polymerase 2
A: Histone PARylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9663
Polymers68,4292
Non-polymers5381
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-15 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.622, 115.622, 143.607
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Poly [ADP-ribose] polymerase 2,Poly [ADP-ribose] polymerase 2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP-ribosyltransferase PARP2 ...hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / DNA ADP-ribosyltransferase PARP2 / NAD(+) ADP-ribosyltransferase 2 / ADPRT-2 / Poly[ADP-ribose] synthase 2 / pADPRT-2 / Protein poly-ADP-ribosyltransferase PARP2


Mass: 31675.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein Histone PARylation factor 1


Mass: 36753.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPF1, C4orf27 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9NWY4
#3: Chemical ChemComp-UHB / 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide


Mass: 537.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N9O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.05 Å3/Da / Density % sol: 69.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES pH 6, 25% v/v pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.96→100.13 Å / Num. obs: 45403 / % possible obs: 100 % / Redundancy: 10.41 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Net I/av σ(I): 14 / Net I/σ(I): 14
Reflection shellResolution: 2.96→3.07 Å / Redundancy: 10.77 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4528 / CC1/2: 0.96 / % possible all: 99.35

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXdev_3126refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo human HPF1

Resolution: 2.96→47.275 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 45.36
RfactorNum. reflection% reflection
Rfree0.2596 1048 4.73 %
Rwork0.2292 --
obs0.2307 22155 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 232.19 Å2 / Biso mean: 154.0346 Å2 / Biso min: 117.99 Å2
Refinement stepCycle: final / Resolution: 2.96→47.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 39 0 4518
Biso mean--146.91 --
Num. residues----555
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9601-3.11620.51391490.4961295596
3.1162-3.31130.44491620.3988293196
3.3113-3.56690.40211010.3118299596
3.5669-3.92570.321530.2574299197
3.9257-4.49340.26691760.219302399
4.4934-5.65970.26521360.21873093100
5.6597-47.2750.20611710.18873119100

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