Literature summary for 3.2.1.143 extracted from

Wang, M.; Yuan, Z.; Xie, R.; Ma, Y.; Liu, X.; Yu, X.
Structure-function analyses reveal the mechanism of the ARH3-dependent hydrolysis of ADP-ribosylation (2018), J. Biol. Chem., 293, 14470-14480 .

Search for more literature for 3.2.1.143

Cloned(Commentary)

Cloned (Comment)	Organism
gene ADPRHL2, sequence comparisons, recombinant expression of N-terminally His-tagged wild-type enzyme and GST-tagged mutant enzymes in Escherichia coli strain BL21(DE3)	Homo sapiens

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified ARH3-ADPR substrate complex, sitting drop vapour diffusion method, ARH3 and ADPR are mixed in the molar ratio of 1:3, mixing of equal volumes of 11 mg/ml protein complex in 10 mM Tris-HCl, pH 8.0, and 100 mM NaCl with reservoir solution consisting of 0.1 M MES, pH 6.0, and 20% w/v PEG MME 2000, addition of 0.2 M non-detergent sulfobetaine NDSB-201, 20°C, X-ray diffraction structure determination and analysis at 1.58 A resolution, molecular replacement using the structure of apo-ARH3 (PDB ID 2FOZ) as the search model, modeling	Homo sapiens

Crystallization (Comment)

Organism

purified ARH3-ADPR substrate complex, sitting drop vapour diffusion method, ARH3 and ADPR are mixed in the molar ratio of 1:3, mixing of equal volumes of 11 mg/ml protein complex in 10 mM Tris-HCl, pH 8.0, and 100 mM NaCl with reservoir solution consisting of 0.1 M MES, pH 6.0, and 20% w/v PEG MME 2000, addition of 0.2 M non-detergent sulfobetaine NDSB-201, 20°C, X-ray diffraction structure determination and analysis at 1.58 A resolution, molecular replacement using the structure of apo-ARH3 (PDB ID 2FOZ) as the search model, modeling

Homo sapiens

Protein Variants

Protein Variants	Comment	Organism
D314A	site-directed mutagenesis, the mutation impairs ARH3-dependent DNA damage repair	Homo sapiens
D77N	site-directed mutagenesis, the mutation impairs ARH3-dependent DNA damage repair	Homo sapiens
E41Q	site-directed mutagenesis, the mutation impairs ARH3-dependent DNA damage repair	Homo sapiens
H182A	site-directed mutagenesis, the mutation impairs ARH3-dependent DNA damage repair	Homo sapiens
additional information	enzyme knockout by expression of ARH3 siRNA in U2OS cells	Homo sapiens
S148A	site-directed mutagenesis, the mutation impairs ARH3-dependent DNA damage repair	Homo sapiens
T317A	site-directed mutagenesis, the mutation impairs ARH3-dependent DNA damage repair	Homo sapiens
Y149A	site-directed mutagenesis, the mutation impairs ARH3-dependent DNA damage repair	Homo sapiens

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required for catalysis, binuclear Mg2+ site, structure overview. The distal ribose of poly(ADP-ribose), enabling the hydroxyl groups of the distal ribose to coordinate the two Mg2+ ions. MgA is coordinated with Asp314, Asp316, Thr317, three hydroxyl groups of the distal ribose and water 269. Meanwhile, MgB is coordinated with the 2'-hydroxyl group of the distal ribose, Thr76, Asp77, Asp78, Asp316, and two water molecules (water 269 and water 85). The sequence alignment and structural comparison reveals that the Mg2+ coordinating acidic residues Asp77, Asp78, Asp314, and Asp316 are fully conserved in homologous ARH enzymes. Both Mg2+ ions are involved in the positioning of water 351 in the catalytic center through hydrogen-bonding interaction. the binding pocket of ARH3 is divided into two subunits by the binuclear Mg2+ sites	Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
poly(ADP-ribose) + H2O	Homo sapiens	-	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	Q9NX46	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged wild-type enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, tag cleavage through rhinovirus 3C (HRV 3C) protease, anion exchange chromatography, gel filtration, and ultrafiltration, recombinant GST-tagged mutant enzymes by glutathione affinity chromatography	Homo sapiens

Reaction

Reaction	Comment	Organism	Reaction ID
(ADP-ribose)n + H2O = (ADP-ribose)n-1 + ADP-ribose	reaction mechanism and structure, overview	Homo sapiens	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
poly(ADP-ribose) + H2O	-	Homo sapiens	?	-	?
poly(ADP-ribose) + H2O	enzyme-substrate binding complex structure analysis, overview	Homo sapiens	?	-	?

Subunits

Subunits	Comment	Organism
More	secondary structure comparisons, overview	Homo sapiens

Synonyms

Synonyms	Comment	Organism
ADPRHL2	-	Homo sapiens
ARH3	-	Homo sapiens

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
22	-	assay at room temperature	Homo sapiens

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.8	-	assay at	Homo sapiens

General Information

General Information	Comment	Organism
additional information	analysis of the catalytic site structure of ARH3, overview	Homo sapiens
physiological function	enzyme ARH3 is a multifunctional enzyme that also hydrolyzes poly(ADP-ribose) (ADPR). Enzyme ARH3 plays a role in DNA damage repair. The recruitment of ARH3 to DNA lesions is mediated by ADPR recognition. The catalytic mechanism of protein ADP-ribose hydrolases can be classified into two different groups, namely metal-dependent and metal-independent catalysis. ARHs, such as ARH3, belong to metal-dependent catalysis, utilizing two Mg2+ ions and acidic residues to complete the catalytic reaction, which might be highly conserved. In contrast, the catalytic mechanism is not conserved in the macrodomain ADP-ribose hydrolases, For example, Glu756 and a water molecule act together to catalyze the reaction in PARG, whereas the key catalytic factor in MacroD2 is an activated water. The charge characteristic of the binding pocket in ARH3 is remarkably distinguished from that in PARG. The binding pocket of PARG, accommodating the ADPR dimer, is mostly composed of the basic region	Homo sapiens