The rise and fall of poly(ADP-ribose): An enzymatic perspective

Abstract

Human cells respond to DNA damage with an acute and transient burst in production of poly(ADP-ribose), a posttranslational modification that expedites damage repair and plays a pivotal role in cell fate decisions. Poly(ADP-ribose) polymerases (PARPs) and glycohydrolase (PARG) are the key set of enzymes that orchestrate the rise and fall in cellular levels of poly(ADP-ribose). In this perspective, we focus on recent structural and mechanistic insights into the enzymes involved in poly(ADP-ribose) production and turnover, and we highlight important questions that remain to be answered.

Keywords: ADP-ribose; DNA damage response; MARG; PARG; PARP; Poly(ADP-ribose).

Figure 1. The rise and fall of poly(ADP-ribose)

The ADP-ribose posttranslational modification regulates many fundamental aspects of human biology. During the DNA damage response, there is an acute and transient burst of poly(ADP-ribose) production and turnover that facilitates repair and contributes to important cell fate signaling events.

Figure 2. DNA damage response PARPs

Three human PARP enzymes are catalytically activated through binding to DNA damage: PARP-1, PARP-2, and PARP-3. The WGR domain and the HD region of the catalytic domain are defining and unique features of the DNA damage-dependent PARPs. PARP-1 consists of multiple domains that assume an active conformation upon binding to DNA damage. Zinc finger domains 1 and 3 (Zn1 and Zn3) interact with a DNA break and pack against the WGR domain, which serves as an intermediary between the C-terminal catalytic and N-terminal DNA binding domains, and allosterically couples damage detection to catalytic activation.

Figure 3. PARG structure and catalytic mechanism

A. The catalytic domain of human poly (ADP-ribose) glycohydrolase PARG (residues 448-976) consists of a macro domain (green; residues 611-812) flanked by N-terminal and C-terminal helical bundles (orange). The high affinity inhibitor adenosine diphosphate hydroxymethyl(pyrrolidinediol) (ADP-HPD; blue) is bound in the active site cleft, flanked by a β-hairpin structure termed the tyrosine clasp (red). Tyrosine 795 from the tyrosine clasp interacts with the α-phosphate of ADP-HPD and ADP-ribose (see panel B). B. The active site of PARG features a catalytic glutamate (Glu 756) and polar residues that engage the ribose and pyrrolidine hydroxyl groups of ADP-HPD and two bound water molecules (red spheres). The bound waters are positioned on either face of the carbon corresponding to the anomeric position of a poly (ADP-ribose) substrate (yellow circle), where they could function as the attacking nucleophile in a retaining (Wat A) or inverting (Wat B) mechanism of hydrolysis. C. Proposed catalytic mechanisms for PARG [43,46] assign Glu 756 as the catalytic acid that protonates the ADP-ribose leaving group, and as the catalytic base that activates a water nucleophile for attack of the anomeric carbon of ribose”. An interaction between the α-phosphorous and the 04″ of ribose (N of the pyrrolidine ring shown here) may stabilize the carbenium intermediate to assist catalysis.