Poly(ADP-ribose) glycohydrolase (PARG) from Drosophila melanogaster in complex with PARG inhibitor PDD00017272

Experimental Data Snapshot

  • Resolution: 2.51 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 

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Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling.

Fontana, P.Buch-Larsen, S.C.Suyari, O.Smith, R.Suskiewicz, M.J.Schutzenhofer, K.Ariza, A.Rack, J.G.M.Nielsen, M.L.Ahel, I.

(2023) Nat Commun 14: 3200-3200

  • DOI: https://doi.org/10.1038/s41467-023-38793-y
  • Primary Citation of Related Structures:  
    8ADJ, 8ADK

  • PubMed Abstract: 

    In the mammalian DNA damage response, ADP-ribosylation signalling is of crucial importance to mark sites of DNA damage as well as recruit and regulate repairs factors. Specifically, the PARP1:HPF1 complex recognises damaged DNA and catalyses the formation of serine-linked ADP-ribosylation marks (mono-Ser-ADPr), which are extended into ADP-ribose polymers (poly-Ser-ADPr) by PARP1 alone. Poly-Ser-ADPr is reversed by PARG, while the terminal mono-Ser-ADPr is removed by ARH3. Despite its significance and apparent evolutionary conservation, little is known about ADP-ribosylation signalling in non-mammalian Animalia. The presence of HPF1, but absence of ARH3, in some insect genomes, including Drosophila species, raises questions regarding the existence and reversal of serine-ADP-ribosylation in these species. Here we show by quantitative proteomics that Ser-ADPr is the major form of ADP-ribosylation in the DNA damage response of Drosophila melanogaster and is dependent on the dParp1:dHpf1 complex. Moreover, our structural and biochemical investigations uncover the mechanism of mono-Ser-ADPr removal by Drosophila Parg. Collectively, our data reveal PARP:HPF1-mediated Ser-ADPr as a defining feature of the DDR in Animalia. The striking conservation within this kingdom suggests that organisms that carry only a core set of ADP-ribosyl metabolising enzymes, such as Drosophila, are valuable model organisms to study the physiological role of Ser-ADPr signalling.

  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly(ADP-ribose) glycohydrolase
A, B, C
578Drosophila melanogasterMutation(s): 0 
Gene Names: PargCG2864
Find proteins for O46043 (Drosophila melanogaster)
Explore O46043 
Go to UniProtKB:  O46043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO46043
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LQX (Subject of Investigation/LOI)
Query on LQX

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
P [auth C]
C23 H26 N6 O4 S2
Query on SO4

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G [auth A]
H [auth A]
I [auth A]
N [auth B]
R [auth C]
G [auth A],
H [auth A],
I [auth A],
N [auth B],
R [auth C],
S [auth C]
O4 S
Query on GOL

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E [auth A],
F [auth A],
L [auth B],
M [auth B],
Q [auth C]
C3 H8 O3
Query on CL

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J [auth A],
O [auth B],
T [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.51 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.392α = 90
b = 115.919β = 112.205
c = 123.267γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210634

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description