6D36

Structure of human ARH3 bound to ADP-ribose and magnesium

Summary for 6D36

• Entry DOI: 10.2210/pdb6d36/pdb
• Descriptor: Poly(ADP-ribose) glycohydrolase ARH3, [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: poly(adp-ribose) hydrolase, hydrolase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 4
• Total formula weight: 159543.55

Authors

Pourfarjam, Y.,Ventura, J.,Kurinov, I.,Kim, I.K. (deposition date: 2018-04-14, release date: 2018-06-20, Last modification date: 2023-10-04)

Primary citation

Pourfarjam, Y.,Ventura, J.,Kurinov, I.,Cho, A.,Moss, J.,Kim, I.K.
Structure of human ADP-ribosyl-acceptor hydrolase 3 bound to ADP-ribose reveals a conformational switch that enables specific substrate recognition.
J.Biol.Chem., 293:12350-12359, 2018

PubMed Abstract: ADP-ribosyl-acceptor hydrolase 3 (ARH3) plays important roles in regulation of poly(ADP-ribosyl)ation, a reversible post-translational modification, and in maintenance of genomic integrity. ARH3 degrades poly(ADP-ribose) to protect cells from poly(ADP-ribose)-dependent cell death, reverses serine mono(ADP-ribosyl)ation, and hydrolyzes -acetyl-ADP-ribose, a product of Sirtuin-catalyzed histone deacetylation. ARH3 preferentially hydrolyzes -linkages attached to the anomeric C1″ of ADP-ribose; however, how ARH3 specifically recognizes and cleaves structurally diverse substrates remains unknown. Here, structures of full-length human ARH3 bound to ADP-ribose and Mg, coupled with computational modeling, reveal a dramatic conformational switch from closed to open states that enables specific substrate recognition. The glutamate flap, which blocks substrate entrance to Mg in the unliganded closed state, is ejected from the active site when substrate is bound. This closed-to-open transition significantly widens the substrate-binding channel and precisely positions the scissile 1″--linkage for cleavage while securing tightly 2″- and 3″-hydroxyls of ADP-ribose. Our collective data uncover an unprecedented structural plasticity of ARH3 that supports its specificity for the 1″--linkage in substrates and Mg-dependent catalysis.

PubMed: 29907568
DOI: 10.1074/jbc.RA118.003586

Experimental method

X-RAY DIFFRACTION (1.7 Å)