8ADJ | pdb_00008adj

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

PDB DOI: https://doi.org/10.2210/pdb8ADJ/pdb

Classification: HYDROLASE
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-08 Released: 2023-06-14
Deposition Author(s): Ariza, A., Fontana, P.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.223 (Depositor), 0.229 (DCC)
R-Value Work:
0.183 (Depositor), 0.189 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

PubMed: 37268618 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-38793-y
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 200.67 kDa
Atom Count: 12,890
Modeled Residue Count: 1,545
Deposited Residue Count: 1,734
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ADP-ribose) glycohydrolase	A, B, C	578	Drosophila melanogaster	Mutation(s): 0 Gene Names: Parg, CG2864 EC: 3.2.1.143 (PDB Primary Data), 3.2.2 (UniProt)
UniProt
Find proteins for O46043 (Drosophila melanogaster) Explore O46043 Go to UniProtKB: O46043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O46043
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LQX (Subject of Investigation/LOI) Query on LQX Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth C] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B]	D [auth A], K [auth B], P [auth C]	1-[(2,5-dimethylpyrazol-3-yl)methyl]-N-(1-methylcyclopropyl)-3-[(2-methyl-1,3-thiazol-5-yl)methyl]-2,4-bis(oxidanylidene)quinazoline-6-sulfonamide C₂₃ H₂₆ N₆ O₄ S₂ IFWUBRBMMNTBRZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain P [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain I [auth A]	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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth A], L [auth B], M [auth B], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C]	J [auth A], O [auth B], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C] Interactions & Density Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C]