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

Johannes Gregor Matthias Rack,Antonio Ariza,Bryon S Drown,Callum Henfrey,Edward Bartlett,Tomohiro Shirai,Paul J Hergenrother,Ivan Ahel

doi:10.1016/j.chembiol.2018.11.001

Johannes Gregor Matthias Rack, Antonio Ariza + Show 6 more

Open Access

https://doi.org/10.1016/j.chembiol.2018.11.001

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Abstract

SummaryProtein ADP-ribosylation is a highly dynamic post-translational modification. The rapid turnover is achieved, among others, by ADP-(ribosyl)hydrolases (ARHs), an ancient family of enzymes that reverses this modification. Recently ARHs came into focus due to their role as regulators of cellular stresses and tumor suppressors. Here we present a comprehensive structural analysis of the enzymatically active family members ARH1 and ARH3. These two enzymes have very distinct substrate requirements. Our data show that binding of the adenosine ribose moiety is highly diverged between the two enzymes, whereas the active sites harboring the distal ribose closely resemble each other. Despite this apparent similarity, we elucidate the structural basis for the selective inhibition of ARH3 by the ADP-ribose analogues ADP-HPD and arginine-ADP-ribose. Together, our biochemical and structural work provides important insights into the mode of enzyme-ligand interaction, helps to understand differences in their catalytic behavior, and provides useful tools for targeted drug design.

Highlights

ADP-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 (Fehr et al, 2017; Gupte et al, 2017; Palazzo et al, 2017)
LchARH3 and hARH1 share low sequence conservation (20.1% identity, 33.4% similarity) and an overall structural root mean square deviation (RMSD) of 3.2 Aover 160 Ca. Models of both enzymes follow the earlier observed fold of a tightly packed, mainly a-orthogonal bundle separated into four quasidomains (A–D) with a binuclear Mg2+ center (Figures 1D and 1E)
Later crystals were grown in the presence of MgCl2, which promoted coordination of a second Mg2+ ion in the LchARH3:ADPr structure, but not the apo form

Summary

Introduction

ADP-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 (Fehr et al, 2017; Gupte et al, 2017; Palazzo et al, 2017). It is established by the stereospecific transfer of ADP-ribose (ADPr) from b-NAD+ onto a target residue, which results in the formation of an a-anomeric ADP-ribosylated amino acid and the release of nicotinamide (Sung, 2015). ARH3 can cleave PAR chains, 100-O-acetyl-ADPr and ADPr at the phosphorylated DNA ends, these activities have not been confirmed in vivo so far (Mueller-Dieckmann et al, 2006; Munnur and Ahel, 2017; Ono et al, 2006)

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