(ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition

摘要

class="head no_bottom_margin" id="sec1title">IntroductionADP-ribosylation is a dynamic post-translational modification involved in the regulation of a wide variety of cellular processes, including DNA damage response (DDR), aging, immunity, bacterial metabolism, and many others (, , ). It is established by the stereospecific transfer of ADP-ribose (ADPr) from β-NAD⁺ onto a target residue, which results in the formation of an α-anomeric ADP-ribosylated amino acid and the release of nicotinamide (). In eukaryotes, this reaction is catalyzed by two distinct families of ADP-ribosyltransferases (ARTs) classified by their catalytic motifs as well as their relationship to bacterial exotoxins: (1) cholera toxin-like ARTs (ARTC) containing an R-S-E motif and (2) diphtheria toxin-like ARTs (PARPs, also called ARTDs) containing an H-Y-E motif (, ). Modification of residues containing acidic (glutamate/aspartate), basic (arginine/lysine), hydroxyl (serine), and thiol (cysteine) moieties have been described (, , ). Specificity for these residues is partially the result of distinct structural arrangements in the ART catalytic domain, with ARTCs usually catalyzing the transfer onto arginine residues and PARPs usually modifying acidic residues (, ). Recently, we have shown that for PARPs this canonical activity can be altered in the mammalian DDR through the formation of a complex of PARP1 or PARP2 with histone PARylation factor 1 (HPF1), which leads to a preference for serine modification in many proteins involved in the maintenance of genomic stability (, ). In addition, a subset of PARPs can transfer further ADPr units onto the initial modification, forming polymers of ADPr units, known as poly(ADP-ribosyl) (PAR) modification (A) (). Reversal of the bulk of PAR modification is mediated by poly(ADP-ribosyl)glycohydrolase (PARG) converting the polymer chain to a mono(ADP-ribosyl) (MAR) modification (href="#bib37" rid="bib37" class=" bibr popnode">Lin et al., 1997, href="#bib60" rid="bib60" class=" bibr popnode">Slade et al., 2011). PARG is unable to efficiently cleave the protein-linked ADPr moiety (href="#bib60" rid="bib60" class=" bibr popnode">Slade et al., 2011), which requires a number of other hydrolases. For example, linkages to glutamate/aspartate are hydrolyzed by macrodomain proteins (href="#bib24" rid="bib24" class=" bibr popnode">Jankevicius et al., 2013, href="#bib57" rid="bib57" class=" bibr popnode">Rosenthal et al., 2013, href="#bib58" rid="bib58" class=" bibr popnode">Sharifi et al., 2013), whereas linkages to arginine and serine are cleaved by ARH1 and ARH3, respectively, two members of the structurally unrelated (ADP-ribosyl)hydrolases (ARHs) family (href="#bib15" rid="bib15" class=" bibr popnode">Fontana et al., 2017, href="#bib41" rid="bib41" class=" bibr popnode">Moss et al., 1988) (href="/pmc/articles/PMC6309922/figure/fig1/" target="figure" class="fig-table-link figpopup" rid-figpopup="fig1" rid-ob="ob-fig1" co-legend-rid="lgnd_fig1">Figure 1A). In addition, ARH3 can cleave PAR chains, 1″-O-acetyl-ADPr and ADPr at the phosphorylated DNA ends, although these activities have not been confirmed in vivo so far (href="#bib42" rid="bib42" class=" bibr popnode">Mueller-Dieckmann et al., 2006, href="#bib45" rid="bib45" class=" bibr popnode">Munnur and Ahel, 2017, href="#bib49" rid="bib49" class=" bibr popnode">Ono et al., 2006).href="/pmc/articles/PMC6309922/figure/fig1/" target="figure" rid-figpopup="fig1" rid-ob="ob-fig1">class="inline_block ts_canvas" href="/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=6309922_gr1.jpg" target="tileshopwindow">target="object" href="/pmc/articles/PMC6309922/figure/fig1/?report=objectonly">Open in a separate windowclass="figpopup" href="/pmc/articles/PMC6309922/figure/fig1/" target="figure" rid-figpopup="fig1" rid-ob="ob-fig1">Figure 1Functional and Structural Overview of ARH1 and ARH3(A) Scheme of vertebrate ADP-ribosylation reactions. The modification of a target protein can occur as MARylation on arginine residues (orange) catalyzed by ARTCs, as well as MARylation and PARylation on glutamate/aspartate (blue) and serine (green) residues catalyzed by PARPs. Arginine de-modification is catalyzed by ARH1, PARylation is removed by PARG and to a lesser extend ARH3, MARylation on glutamate/aspartate residues is hydrolyzed by macrodomain proteins, whereas the terminal modification on serine residues is removed by ARH3.(B) Pairwise sequence identity comparison of selected ARH3 proteins. Sequence identity and similarity (in parentheses) are provided.(C) (ADP-ribosyl)hydrolase activity assessment of selected ARH3 orthologues. All ARH3s efficiently remove MARylation from the histone H3 peptide (aa 1-20) and degrade PARP1 generated PARylation to a variable extent.(D) Ribbon representation of hARH1 and LchARH3 in complex with ADPr (red) showing quasidomains A (orange), B (yellow), C (blue), and D (green) as well as the coordinated Mg²⁺ ions (cyan).(E) Liquorice-surface representation of hARH1 and LchARH3 (brown) in complex with ADPr (black). Residues important for the interaction are highlighted (see href="#mmc1" rid="mmc1" class=" supplementary-material">Figures S1–S3 for further details).See also href="#mmc1" rid="mmc1" class=" supplementary-material">Figures S1–S3.