6TVH

Selenomethionine-substituted HPF1 from Nematostella vectensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

HPF1 completes the PARP active site for DNA damage-induced ADP-ribosylation.

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.

(2020) Nature 579: 598-602

  • DOI: https://doi.org/10.1038/s41586-020-2013-6
  • Primary Citation of Related Structures:  
    6TVH, 6TX1, 6TX2, 6TX3

  • PubMed Abstract: 

    The anti-cancer drug target poly(ADP-ribose) polymerase 1 (PARP1) and its close homologue, PARP2, are early responders to DNA damage in human cells 1,2 . After binding to genomic lesions, these enzymes use NAD + to modify numerous proteins with mono- and poly(ADP-ribose) signals that are important for the subsequent decompaction of chromatin and the recruitment of repair factors 3,4 . These post-translational modifications are predominantly serine-linked and require the accessory factor HPF1, which is specific for the DNA damage response and switches the amino acid specificity of PARP1 and PARP2 from aspartate or glutamate to serine residues 5-10 . Here we report a co-structure of HPF1 bound to the catalytic domain of PARP2 that, in combination with NMR and biochemical data, reveals a composite active site formed by residues from HPF1 and PARP1 or PARP2 . The assembly of this catalytic centre is essential for the addition of ADP-ribose moieties after DNA damage in human cells. In response to DNA damage and occupancy of the NAD + -binding site, the interaction of HPF1 with PARP1 or PARP2 is enhanced by allosteric networks that operate within the PARP proteins, providing an additional level of regulation in the induction of the DNA damage response. As HPF1 forms a joint active site with PARP1 or PARP2, our data implicate HPF1 as an important determinant of the response to clinical PARP inhibitors.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted protein
A, B
336Nematostella vectensisMutation(s): 0 
Gene Names: v1g201271
UniProt
Find proteins for A7RS11 (Nematostella vectensis)
Explore A7RS11 
Go to UniProtKB:  A7RS11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7RS11
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.948α = 90
b = 88.948β = 90
c = 224.097γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2020-02-19 
  • Deposition Author(s): Ariza, A.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101794
Wellcome TrustUnited Kingdom210634
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R007195/1
Cancer Research UKUnited KingdomC35050/A22284

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary