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Literature summary extracted from

  • Zha, M.; Guo, Q.; Zhang, Y.; Yu, B.; Ou, Y.; Zhong, C.; Ding, J.
    Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies (2008), J. Mol. Biol., 379, 568-578.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.6.1.13
-
 Homo sapiens
3.6.1.13 overexpression of wild-type and mutant enzymes Homo sapiens

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.6.1.13 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 Homo sapiens
3.6.1.13 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 Homo sapiens

Protein Variants

EC Number Protein Variants Comment Organism
3.6.1.13 C139A site-directed mutagenesis, mutation causes a 2.1fold increase in Km for ADP-ribose but has no effect on kcat compared to the wild-type enzyme Homo sapiens
3.6.1.13 C139A the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 D133A site-directed mutagenesis, mutation causes a 4.0fold increase in Km for ADP-ribose but has no effect on kcat compared to the wild-type enzyme Homo sapiens
3.6.1.13 D133A the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 D133N site-directed mutagenesis, mutation causes a 2.1fold increase in Km for ADP-ribose but has no effect on kcat compared to the wild-type enzyme Homo sapiens
3.6.1.13 D133N the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 D164A the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 D164N the mutant shows increased catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 E112Q the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 E115Q the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 E116Q the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 E166Q the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 E93Q site-directed mutagenesis, mutation causes a 1.8fold increase in Km for ADP-ribose but has no effect on kcat compared to the wild-type enzyme Homo sapiens
3.6.1.13 E93Q the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 L98A site-directed mutagenesis, mutation of Leu98 to Ala causes a 5.8fold increase in Km but has no effect on kcat compared to the wild-type enzyme Homo sapiens
3.6.1.13 L98A the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 additional information construction of a truncation mutant DELTAhNUDT5 Homo sapiens
3.6.1.13 Q82A the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 R111Q the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 R196Q site-directed mutagenesis, mutation causes a 5.5fold increase in Km for ADP-ribose but has no effect on kcat compared to the wild-type enzyme Homo sapiens
3.6.1.13 R196Q the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 R51Q site-directed mutagenesis, the mutant shows a 14.6fold increased Km and a 17fold decreased kcat for ADP-ribose compared to the wild-type enzyme Homo sapiens
3.6.1.13 R51Q the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 R84Q the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 W28A site-directed mutagenesis, the mutant shows 8.4fold increased Km for ADP-ribose, but unaltered kcat compared to the wild-type enzyme Homo sapiens
3.6.1.13 W28A the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 W28A/W46A site-directed mutagenesis, the mutant shows 53.7fold increased Km and a 219fold decreased kcat for ADP-ribose compared to the wild-type enzyme Homo sapiens
3.6.1.13 W28A/W46A the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
3.6.1.13 W46A site-directed mutagenesis, the mutant shows 5.7fold increased Km for ADP-ribose, but unaltered kcat compared to the wild-type enzyme Homo sapiens
3.6.1.13 W46A the mutant shows reduced catalytic efficiency compared to the wild type enzyme Homo sapiens

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.6.1.13 additional information
-
 additional information kinetic analysis, Trp28 and Trp46 function synergistically in substrate binding and catalysis, overview Homo sapiens
3.6.1.13 0.0209
-
 ADP-D-ribose mutant enzyme D164N, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0223
-
 ADP-ribose pH 7.0, 37°C, wild-type enzyme Homo sapiens
3.6.1.13 0.0223
-
 ADP-D-ribose wild type enzyme, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0231
-
 ADP-D-ribose mutant enzyme E166Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0257
-
 ADP-D-ribose mutant enzyme E116Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0279
-
 ADP-D-ribose mutant enzyme R111Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0389
-
 ADP-D-ribose mutant enzyme E93Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0402
-
 ADP-D-ribose mutant enzyme E115Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0434
-
 ADP-D-ribose mutant enzyme D164A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0456
-
 ADP-D-ribose mutant enzyme D133N, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0463
-
 ADP-D-ribose mutant enzyme C139A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0702
-
 ADP-D-ribose mutant enzyme E112Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0879
-
 ADP-D-ribose mutant enzyme D133A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.1084
-
 ADP-D-ribose mutant enzyme R84Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.1197
-
 ADP-D-ribose mutant enzyme R196Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.1265
-
 ADP-D-ribose mutant enzyme W46A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.1271
-
 ADP-D-ribose mutant enzyme Q82A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.1283
-
 ADP-D-ribose mutant enzyme L98A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.1497
-
 ADP-D-ribose mutant enzyme W28A/W46A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.184
-
 ADP-D-ribose mutant enzyme W28A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.3213
-
 ADP-D-ribose mutant enzyme R51Q, at pH 7.0 and 37°C Homo sapiens

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.6.1.13 Mg2+ required Homo sapiens

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.6.1.13 ADP-D-ribose + H2O Homo sapiens
-
 AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 ADP-ribose + H2O Homo sapiens the enzyme plays important roles in controlling the intracellular levels of ADPR and preventing non-enzymatic ADP-ribosylation of proteins by hydrolyzing ADPR to AMP and ribose 5?-phosphate AMP + D-ribose 5-phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.6.1.13 Homo sapiens
-
-
-
3.6.1.13 Homo sapiens Q9UKK9
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.6.1.13
-
 Homo sapiens

Reaction

EC Number Reaction Comment Organism Reaction ID
3.6.1.13 ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate molecular catalytic mechanism involving Arg51, Arg111, Glu112, and Glu116, active site structure, substrate binding involving Arg51, Leu98, Trp28 and Trp46 and transition-state structure, structure-function relationship, and kinetic analysis Homo sapiens
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.6.1.13 ADP-D-ribose + H2O
-
 Homo sapiens AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 ADP-ribose + H2O preferred substrate Homo sapiens AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 ADP-ribose + H2O the enzyme plays important roles in controlling the intracellular levels of ADPR and preventing non-enzymatic ADP-ribosylation of proteins by hydrolyzing ADPR to AMP and ribose 5?-phosphate Homo sapiens AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 additional information hNUDT5 can utilize a variety of ADP-sugar conjugates as substrate, with a preference for ADPR Homo sapiens ?
-
 ?

Subunits

EC Number Subunits Comment Organism
3.6.1.13 dimer homodimer Homo sapiens

Synonyms

EC Number Synonyms Comment Organism
3.6.1.13 ADP-ribose pyrophosphatase
-
 Homo sapiens
3.6.1.13 ADPR pyrophosphatase
-
 Homo sapiens
3.6.1.13 ADPRase
-
 Homo sapiens
3.6.1.13 NUDT5
-
 Homo sapiens

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.6.1.13 37
-
 assay at Homo sapiens

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.6.1.13 0.0019
-
 ADP-D-ribose mutant enzyme E112Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.0069
-
 ADP-D-ribose mutant enzyme E116Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.058
-
 ADP-D-ribose mutant enzyme W28A/W46A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.1
-
 ADP-D-ribose mutant enzyme E166Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.18
-
 ADP-D-ribose mutant enzyme R84Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.32
-
 ADP-D-ribose mutant enzyme R111Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.41
-
 ADP-D-ribose mutant enzyme R51Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 2.7
-
 ADP-D-ribose mutant enzyme E115Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 4.5
-
 ADP-D-ribose mutant enzyme E93Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 6
-
 ADP-D-ribose mutant enzyme R196Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 7.3
-
 ADP-D-ribose mutant enzyme D133A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 10.3
-
 ADP-D-ribose mutant enzyme Q82A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 10.4
-
 ADP-D-ribose mutant enzyme D133N, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 11.3
-
 ADP-D-ribose mutant enzyme W46A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 11.4
-
 ADP-ribose pH 7.0, 37°C, wild-type enzyme Homo sapiens
3.6.1.13 11.8
-
 ADP-D-ribose wild type enzyme, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 12.2
-
 ADP-D-ribose mutant enzyme D164A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 12.4
-
 ADP-D-ribose mutant enzyme L98A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 13.1
-
 ADP-D-ribose mutant enzyme D164N, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 13.3
-
 ADP-D-ribose mutant enzyme W28A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 13.7
-
 ADP-D-ribose mutant enzyme C139A, at pH 7.0 and 37°C Homo sapiens

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.6.1.13 7
-
 assay at Homo sapiens

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.6.1.13 0.0027
-
 ADP-D-ribose mutant enzyme E112Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.005
-
 ADP-D-ribose mutant enzyme W28A/W46A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 0.23
-
 ADP-D-ribose mutant enzyme E116Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 1.2
-
 ADP-D-ribose mutant enzyme R51Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 1.7
-
 ADP-D-ribose mutant enzyme R84Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 4.3
-
 ADP-D-ribose mutant enzyme E166Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 13
-
 ADP-D-ribose mutant enzyme R111Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 50
-
 ADP-D-ribose mutant enzyme R196Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 67
-
 ADP-D-ribose mutant enzyme E115Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 72
-
 ADP-D-ribose mutant enzyme W28A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 81
-
 ADP-D-ribose mutant enzyme Q82A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 83
-
 ADP-D-ribose mutant enzyme D133A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 89
-
 ADP-D-ribose mutant enzyme W46A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 97
-
 ADP-D-ribose mutant enzyme L98A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 120
-
 ADP-D-ribose mutant enzyme E93Q, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 230
-
 ADP-D-ribose mutant enzyme D133N, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 300
-
 ADP-D-ribose mutant enzyme C139A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 390
-
 ADP-D-ribose mutant enzyme D164A, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 530
-
 ADP-D-ribose wild type enzyme, at pH 7.0 and 37°C Homo sapiens
3.6.1.13 630
-
 ADP-D-ribose mutant enzyme D164N, at pH 7.0 and 37°C Homo sapiens