9BPY | pdb_00009bpy

Human PARP1 ART domain bound to NAD+ analogs benzamide adenine dinucleotide and carba-NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CNAClick on this verticalbar to view detailsBest fitted DQVClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

PARP enzyme de novo synthesis of protein-free poly(ADP-ribose).

Langelier, M.F.Mirhasan, M.Gilbert, K.Sverzhinksy, A.Furtos, A.Pascal, J.M.

(2024) Mol Cell 84: 4758-4773.e6

  • DOI: https://doi.org/10.1016/j.molcel.2024.10.024
  • Primary Citation of Related Structures:  
    9BPY, 9DMC

  • PubMed Abstract: 

    PARP enzymes transfer ADP-ribose from NAD + onto proteins as a covalent modification that regulates multiple aspects of cell biology. Here, we identify an undiscovered catalytic activity for human PARP1: de novo generation of free PAR molecules that are not attached to proteins. Free PAR production arises when a molecule of NAD + or ADP-ribose docks in the PARP1 acceptor site and attaches to an NAD + molecule bound to the donor site, releasing nicotinamide and initiating ADP-ribose chains that emanate from NAD + /ADP-ribose rather than protein. Free PAR is also produced by human PARP2 and the PARP enzyme Tankyrase. We demonstrate that free PAR in cells is generated mostly by PARP1 de novo synthesis activity rather than by PAR-degrading enzymes PAR glycohydrolase (PARG), ARH3, and TARG1 releasing PAR from protein. The coincident production of free PAR and protein-linked modifications alters models for PAR signaling and broadens the scope of PARP enzyme signaling capacity.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1
A, B, C, D
271Homo sapiensMutation(s): 0 
Gene Names: PARP1ADPRTPPOL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens)
Explore P09874 
Go to UniProtKB:  P09874
PHAROS:  P09874
GTEx:  ENSG00000143799 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09874
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.664α = 98.49
b = 74.142β = 105.16
c = 85.182γ = 104.8
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CNAClick on this verticalbar to view detailsBest fitted DQVClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT173370

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release