Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase

Abstract

Poly(ADP-ribosyl)ation is a reversible post-translational protein modification involved in the regulation of a number of cellular processes including DnA repair, chromatin structure, mitosis, transcription, checkpoint activation, apoptosis and asexual development. The reversion of poly(ADP-ribosyl)ation is catalysed by poly(ADP-ribose) (PAR) glycohydrolase (PARG), which specifically targets the unique PAR (1′′-2′) ribose-ribose bonds. Here we report the structure and mechanism of the first canonical PARG from the protozoan Tetrahymena thermophila. In addition, we reveal the structure of T. thermophila PARG in a complex with a novel rhodaninecontaining mammalian PARG inhibitor RBPI-3. our data demonstrate that the protozoan PARG represents a good model for human PARG and is therefore likely to prove useful in guiding structure-based discovery of new classes of PARG inhibitors.

Structures and Mechanisms of Enzymes Employed in the Synthesis and Degradation of PARP-Dependent Protein ADP-Ribosylation

“…Furthermore, such studies also provide the means to develop inhibitors against specific PARPs as important tools to study these processes, but these inhibitors are already making their way into the clinic to treat specific types of cancers as well as cardiovascular and neurodegenerative diseases (Papeo et al, 2013). Inhibiting PAR degrading enzymes has also been proposed as an alternative approach in the clinic (Dunstan et al, 2012;Min and Wang, 2009). The specificity of such inhibitors is highly important; therefore, furthering our insight into the structure and function of the remaining PARPs and other proteins involved in ADP-ribosylation signaling would benefit the drug design efforts.…”

“…Human as well as other vertebrate PARGs are composed of three domains: two of these domains, namely macrodomain and the PARG accessory domain, make up the minimal PARG catalytic region, while the third domain, which shows significantly less sequence conservation, is the putative PARG regulatory region (Figure 4) (Dunstan et al, 2012;Patel et al, 2005;Slade et al, 2011;Tucker et al, 2012). The latter regulatory domain is absent in PARGs of the majority of eukaryotes, and it is not important for PAR hydrolysis in vitro (Botta and Jacobson, 2010;Slade et al, 2011).…”

“…Similarly to other macrodomains, the macrodomain in the PARG catalytic region also has a compact globular shape with a central 7-stranded mixed b sheet flanked by five a helices, packed onto both sides of the sheet, with one helix present at the ridge of the sheet (Dunstan et al, 2012;Kim et al, 2012;Slade et al, 2011;Tucker et al, 2012;Wang et al, 2014). In addition, in all canonical macrodomain proteins, including PARG, the ADP-ribose binding sites are typically situated at a crest of the globular domain, with central phosphates typically buried inside a tunnel ( Figure 5).…”

Identification, biochemical characterization, and in-vivo expression of the intracellular invertase BfrA from the pathogenic parasite Leishmania major

“…Dynamic docking of substrate into BfrA active site was performed as previously reported for other proteins-ligand complexes models. [52][53][54] Ligands were placed in BfrA model active site using fructose orientation in 3PIJ X-ray structure. The complex was then equilibrated by keeping protein backbone restrained on the model conformation.…”

At the Interface of Three Nucleic Acids: The Role of RNA-Binding Proteins and Poly(ADP-ribose) in DNA Repair

“…Since degradation occurs when the polymer is available, PAR-binding proteins can potentially counteract PARG. PARG is actually unable to cleave the proximal ADP-ribose monomer, which appears to be due to steric hindrance [163]. ADP-ribose units are removed from mono(ADP-ribosyl)ated proteins by specific enzymes [164].…”