6BHV

Human PARP-1 bound to NAD+ analog benzamide adenine dinucleotide (BAD)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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Literature

NAD+analog reveals PARP-1 substrate-blocking mechanism and allosteric communication from catalytic center to DNA-binding domains.

Langelier, M.F., Zandarashvili, L., Aguiar, P.M., Black, B.E., Pascal, J.M.

(2018) Nat Commun 9: 844-844

  • DOI: 10.1038/s41467-018-03234-8
  • Primary Citation of Related Structures:  
    6BHV

  • PubMed Abstract: 

    • PARP-1 cleaves NAD + and transfers the resulting ADP-ribose moiety onto target proteins and onto subsequent polymers of ADP-ribose. An allosteric network connects PARP-1 multi-domain detection of DNA damage to catalytic domain structural changes that relieve catalytic autoinhibition; however, the mechanism of autoinhibition is undefined ...

    PARP-1 cleaves NAD + and transfers the resulting ADP-ribose moiety onto target proteins and onto subsequent polymers of ADP-ribose. An allosteric network connects PARP-1 multi-domain detection of DNA damage to catalytic domain structural changes that relieve catalytic autoinhibition; however, the mechanism of autoinhibition is undefined. Here, we show using the non-hydrolyzable NAD + analog benzamide adenine dinucleotide (BAD) that PARP-1 autoinhibition results from a selective block on NAD + binding. Following DNA damage detection, BAD binding to the catalytic domain leads to changes in PARP-1 dynamics at distant DNA-binding surfaces, resulting in increased affinity for DNA damage, and providing direct evidence of reverse allostery. Our findings reveal a two-step mechanism to activate and to then stabilize PARP-1 on a DNA break, indicate that PARP-1 allostery influences persistence on DNA damage, and have important implications for PARP inhibitors that engage the NAD + binding site.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada. john.pascal@umontreal.ca.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1A, B, C, D271Homo sapiensMutation(s): 0 
Gene Names: PARP1, ADPRT, PPOL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens)
Explore P09874 
Go to UniProtKB:  P09874
PHAROS:  P09874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09874
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DQV
Query on DQV
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]		[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
C22 H28 N6 O14 P2
HNKKJJHKTPALEK-RACQCECLSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DQV Binding MOAD:  6BHV Kd: 5870 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.51α = 98.66
b = 75.356β = 104.94
c = 85.607γ = 106.73
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada142354

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence