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3.6.1.13: ADP-ribose diphosphatase

This is an abbreviated version!
For detailed information about ADP-ribose diphosphatase, go to the full flat file.

Word Map on EC 3.6.1.13

Reaction

ADP-D-ribose
+
H2O
=
AMP
 +
D-ribose 5-phosphate

Synonyms

adenosine 5'-diphosphosugar pyrophosphatase, adenosine diphosphoribose pyrophosphatase, ADP-ribose diphosphatase, ADP-ribose hydrolase, ADP-ribose phosphohydrolase, ADP-ribose pyrophosphatase, ADP-ribose pyrophosphatase Sll1054, ADP-ribose pyrophosphatase Slr0920, ADP-ribose pyrophosphatase Slr1134, ADP-ribose pyrophosphatase-I, ADP-ribose/CDP-alcohol diphosphatase, ADP-ribose/NADH pyrophosphohydrolase, ADPR pyrophosphatase, ADPR-PPase, ADPRase, ADPRase-I, ADPRibase, ADPRibase-Mn, ADPribose pyrophosphatase, Adprm, AT4G12720, AtNUDT10, AtNUDT2, AtNUDT6, AtNUDT7, AtNUDX7, cADPR phosphohydrolase, CinA, cyclic ADPR phosphohydrolase, DR2204, EcADPRase, mNUDT5 protein, More, MT1739, MtADPRase, MutT/nudix family protein, NadM-Nudix, Ndx2, Ndx4, NMN adenylyltransferase/ADP-ribose pyrophosphatase, Nudix hydrolase, Nudix hydrolase 7, NUDT5, NUDT5 protein, NUDT9, NUDT9 protein, NUDT9alpha protein, NUDX2, NUDX7, NuhA, pyrophosphatase, adenosine diphosphoribose, submicromolar-K(m) ADP-ribose pyrophosphatase, TtADPRase, YSA1H, zgc:64213

ECTree

     3 Hydrolases
         3.6 Acting on acid anhydrides
             3.6.1 In phosphorus-containing anhydrides
                3.6.1.13 ADP-ribose diphosphatase

Crystallization

Crystallization on EC 3.6.1.13 - ADP-ribose diphosphatase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
substrate-docking to zebrafish wild-type protein, and H97A mutant point to a role of His-97 in catalysis by orientation, and to a bidentate water bridging the dinuclear metal center as the potential nucleophile
gadolinium derivative, to 2.0 A resolution. The crystal structure of DR2204 consists of the conserved alpha/beta/alpha sandwich fold typical of Nudix hydrolases, the Nudix box, residues 94-115, holding the alpha1 helix sits between two loops accessible to the solvent, while the other two helices, alpha2 and alpha3, lie on the other side of the central beta-sheet and participate in dimer-interface formation
hanging-drop vapor diffusion at 18°C. The structure of the apo enzyme, the active enzyme and the complex with ADP-ribose are determined to 1.9 A, 2.7 A and 2.3 A, respectively. The Nudix motif residues, folded as a loop-helix-loop tailored for diphosphate hydrolysis, compose the catalytic center
purified recombinant enzyme in complex with the product AMP and Mn2+ ions in its Nudix active site, sitting drop vapor diffusion method, 20°C, 0.001 ml of 15 mg/ml protein solution is mixed with an equal volume of reservoir solution containing 0.1 M Tris, pH 7.5, 200 mM MgCl2, and 19% PEG 3350, with or without 30 mM AMP, equilibration against the reservoir, X-ray diffraction structure determination and analysis at 2.3 A resolution, molecular replacement method
complexed with 8-oxo-dGMP, 8-oxo-dGDP and 8-oxo-dADP, hanging drop vapor diffusion method, using 0.8 M NaH2PO4/1.2M K2HPO4 and 0.1 M acetate (pH 4.5), and 0.2M ammonium acetate, 35-40% (w/v) polyethylene glycol 3350 and 0.1 M sodium citrate (pH 6.2)
in apo form, in complex with ADP-D-ribose, and in complex with AMP with bound Mg2+, hanging drop vapor diffusion method, using 160 mM sodium acetate (pH 5.5), and 25% (w/v) 2-methyl-2,4-pentanediol, or 300 mM di-ammonium hydrogen citrate, 6% (w/v) n-propanol and 15% (w/v) polyethylene glycol 3350, or 200 mM sodium acetate, 100 mM Tris-HCl (pH 8.0) and 30% (w/v) polyethylene glycol 4000
in complex with alpha,beta-methyleneadenosine diphosphoribose and 3 Mg2+ ions, hanging drop vapor diffusion method, using 250 mM sodium acetate, 100 mM Tris-HCl, pH 8.0, and 29% (w/v) polyethylene glycol 4000
purified recombinant wild-type and truncated mutant NUDT5 in complex with a non-hydrolyzable ADPR analogue, alpha,beta-methyleneadenosine diphosphoribose, and three Mg2+ ions representing the transition state of the enzyme during catalysis, 20 mg/ml protein is incubated with 5 mM AMPCPR and 10 mM MgCl2 at 4 °C overnight, followed by hanging drop vapour diffusion method, wild-type enzyme in complex with AMPCPR, and truncation mutant DELTAhNUDT5 in complex with AMPCPR and Mg2+, 4 °C, mixing of equal volumes of the protein solution and the reservoir solution containing 250 mM NaAc, 100 mM Tris-HCl, pH 8.0, and 29% PEG 4000, ingle crystals of the plate-shape morphology grow after 1 month, X-ray diffraction structure determination and anaylsis at 2.0 A resolution, molecular modelling
substrate docking on a homology model suggests possible interactions of ADP-ribose with seven residues located, with one exception (Cys253), either within the metallo-dependent phosphatases signature (Gln27, Asn110, His111), or in unique structural regions of the ADPRibase-Mn family: s2s3 (Phe37 and Arg43) and h7h8 (Phe210), around the active site entrance. Residue Phe37 is needed for ADP-ribose preference without catalytic effect. Arg43 is essential for catalysis. Cys253 is hindering for cADPR phosphohydrolase
purified recombinant His-tagged enzyme in complex with co-purified NAD and diphosphate complexed in the NadM-domain active site, and with ADPR substrate complexed in the Nudix-domain, hanging drop vapor diffusion method, 0.0015 ml of 15 mg/ml protein solution is mixed with an equal volume of reservoir solution containing 100 mM Tris, pH 7.5, and 1.5 M Li2SO4, 20°C, 3 days to 2 weeks, X-ray diffraction structure determination and analysis at 2.6 A resolution, selenomethionyl MAD phasing method
crystal structures analysis of Ndx4 in the E-state obtained at 0.91 A resolution, PDB IDs are 2YVM, 1MP2, 1G0S, and 2DSB
crystallized in absence or presence of ADP-ribose by hanging-drop vapour-diffusion method. 1.5 A resolution from the apo form using synchrotron radiation and 2.0 A resolution from the complexed form. Both crystals belong to space group P3(1)21 or P3(2)21 and contain one molecule in the asymmetric unit
in complex with alpha,beta-methyleneadenosine diphosphoribose, sitting drop vapor diffusion method, using 18% (w/v) PEG 4000, 0.1 M sodium acetate buffer pH 5.3, 20% (w/v) glycerol, 0.2 M ammonium sulfate, at 20°C
Ndx2 alone and in complex with Mg2+, with Mg2+ and AMP, and with Mg2+ and a nonhydrolyzable ADPR analogue, hanging-drop vapor diffusion method, 20 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 100 mM KCl, 0.001 ml of protein solution is mixed with the equal volume of reservoir solution and equilibrated against the reservoir, containing 0.1 M MES, pH 6.5, 0.16 M sodium acetate or magnesium acetate for the complexed enzyme, 14% PEG 8000, and 20% glycerol, at 20°C, soaking of crystals in 50 mM KAu(CN)2, X-ray diffraction structure determination and anaylsis at 2.0 A resolution, MAD phasing, model building, and refinement
to 2.16 A resolution. The crystal structure shows an unusual asymmetric dimer, with three domains for each chain. The C-terminal domain harbors the nicotinamide mononucleotide deamidase activity. The N-terminal domain belongs to the COG1058 family and is associated with the ADP-ribose diphosphatase activity. The mechanism for the ADP-ribose diphosphatase reaction involves a rotation of the COG1058 domain dimer as part of the reaction cycle
Zn2+-bound enzyme, binary complex with ADPribose, ternary complex with Zn2+ and ADPribose, ternary complex with Gd3+ and ADPribose, product complex with AMP and Mg2+, product complex with ribose 5'-phosphate and Zn2+, mutant enzyme E82Q with ligands Mg2+ and SO42-, mutant enzyme E86Q with ligands Mg2+ and ADPribose, mutant enzyme E82Q with ligands Zn2+ and SO42-, mutant enzyme E86Q with ligands Zn2+ and ADPribose
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