Information on EC 3.6.1.13 - ADP-ribose diphosphatase

for references in articles please use BRENDA:EC3.6.1.13
Word Map on EC 3.6.1.13
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Select one or more organisms in this record:

The enzyme appears in viruses and cellular organisms

top print hide
EC NUMBER
COMMENTARY hide
3.6.1.13
-
top print hide
RECOMMENDED NAME
GeneOntology No.
ADP-ribose diphosphatase
top print hide
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
show the reaction diagram
top print hide
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphorous acid anhydride hydrolysis
-
-
-
-
top print hide
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
purine metabolism
-
-
Purine metabolism
-
-
top print hide
SYSTEMATIC NAME
IUBMB Comments
ADP-D-ribose ribophosphohydrolase
-
top
top print hide
CAS REGISTRY NUMBER
COMMENTARY hide
9024-83-3
-
top print hide
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
Uniprot
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
PCC 7002
SwissProt
Manually annotated by BRENDA team
enzyme displays both nicotinamide mononucleotide deamidase and ADP-ribose diphosphatase activities
UniProt
Manually annotated by BRENDA team
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
top print hide
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
NUDX7 contributes to 23% of the total diphosphohydrolase activity toward ADP-ribose under normal conditions, while under oxidative stress, the contribution of NUDX7 to the activity increases to 34%. Additionally, NUDX7 accounts for 53% of the total pyrophosphohydrolase activity toward NADH under normal conditions and the activity is increased by oxidative stress with NUDX7 contributing 57%
top print hide
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1,Nepsilon-etheno-ADP-ribose + H2O
1,Nepsilon-etheno-AMP-ribose + phosphate
show the reaction diagram
-
fluorogenic substrate
the product is converted to fluorescent 1,Nepsilon-etheno-adenosine by alkaline phosphatase for detection
-
?
2''-O-acetyl-ADP-ribose + H2O
AMP + 2-O-acetyl-D-ribose 5-phosphate
show the reaction diagram
-
-
-
-
?
2',3'-cAMP + H2O
3'AMP
show the reaction diagram
8-oxo-dADP + H2O
?
show the reaction diagram
-
-
-
-
?
8-oxo-dGDP + H2O
8-oxo-dGMP + phosphate
show the reaction diagram
-
-
-
-
?
8-oxo-dGDP + H2O
?
show the reaction diagram
-
-
-
-
?
8-oxo-dGTP + H2O
?
show the reaction diagram
-
the enzyme hardly acts on 8-oxo-dGTP
-
-
?
ADP + H2O
AMP + phosphate
show the reaction diagram
-
-
-
?
ADP-D-ribose + H2O
AMP + D-ribose 5-phosphate
show the reaction diagram
ADP-glucose + H2O
?
show the reaction diagram
ADP-glucose + H2O
AMP + alpha-D-glucose 1-phosphate
show the reaction diagram
ADP-mannose + H2O
AMP + D-mannose 1-phosphate
show the reaction diagram
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
show the reaction diagram
ADP-ribose + H2O
AMP + ribose 5-phosphate
show the reaction diagram
ADPribose + H2O
AMP + D-ribose 5-phosphate
show the reaction diagram
ADPribose 2'-phosphate + H2O
adenosine 2',5'-diphosphate + D-ribose 5-phosphate
show the reaction diagram
-
-
-
-
?
cADP-ribose + H2O
N1-(5-phosphoribosyl)-AMP + phosphate
show the reaction diagram
CDP-choline + H2O
CMP + choline phosphate
show the reaction diagram
CDP-ethanolamine + H2O
CMP + ethanolamine phosphate
show the reaction diagram
-
-
-
-
CDP-glucose + H2O
CMP + glucose 5-phosphate
show the reaction diagram
-
at 5% of the activity with ADPribose
-
-
?
CDP-glycerol + H2O
CMP + glycerol phosphate
show the reaction diagram
-
-
-
-
CDP-ribose + H2O
CMP + D-ribose 5-phosphate
show the reaction diagram
-
kcat/Km is 2.5% of the kcat/Km for ADP-ribose
-
-
?
diadenosine 5',5''-diphosphate + H2O
?
show the reaction diagram
20% the activity with ADP-ribose
-
-
?
FAD + H2O
?
show the reaction diagram
GDP-glucose + H2O
GMP + glucose
show the reaction diagram
7% of the activity with ADP-ribose
-
-
?
GDP-glucose + H2O
GMP + glucose 5-phosphate
show the reaction diagram
GDP-mannose + H2O
GMP + D-mannose 1-phosphate
show the reaction diagram
GDP-ribose + H2O
GMP + D-ribose 5-phosphate
show the reaction diagram
-
kcat/Km is 3% of the kcat/Km for ADP-ribose
-
-
?
IDP-ribose + H2O
IMP + D-ribose 5-phosphate
show the reaction diagram
-
138% of the activity with ADPribose
-
-
?
IDP-ribose + H2O
IMP + ribose 5-phosphate
show the reaction diagram
IDPribose + H2O
IMP + D-ribose 5-phosphate
show the reaction diagram
77% of the activity with ADPribose
-
-
?
NAD+ + H2O
?
show the reaction diagram
-
ADPRibase-Mn in presence of Mn2+, no activity with ADPRibase I and ADPRibase II
-
-
?
NAD+ + H2O
AMP + NMN
show the reaction diagram
7% of the activity with ADP-ribose
-
-
?
NADH + H2O
?
show the reaction diagram
NADH + H2O
AMP + NMNH
show the reaction diagram
NADPH + H2O
AMP + ?
show the reaction diagram
12% of the activity with ADP-ribose
-
-
?
UDP-galactose + H2O
UDP + galactose
show the reaction diagram
7% of the activity with ADP-ribose
-
-
?
UDP-glucose + H2O
UMP + glucose 5-phosphate
show the reaction diagram
UDP-mannose + H2O
UMP + D-mannose 1-phosphate
show the reaction diagram
additional information
?
-
top print hide
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ADP-D-ribose + H2O
AMP + D-ribose 5-phosphate
show the reaction diagram
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
show the reaction diagram
ADP-ribose + H2O
AMP + ribose 5-phosphate
show the reaction diagram
Q9UKK9
the function of the enzyme might be to remove free ADP-ribose arising from NAD+ and protein-bound poly- and non-enzymic protein glycation
-
-
?
ADPribose + H2O
AMP + D-ribose 5-phosphate
show the reaction diagram
FAD + H2O
?
show the reaction diagram
top print hide
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
top print hide
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,N6-ethenoNAD+
-
-
2'-deoxyNAD+
-
-
3'-deoxyNAD+
-
-
3-acetylpyridineNAD+
-
-
5-amino-3-(morpholin-4-yl)-1,2,3-oxadiazol-3-ium
-
3-morpholinosynonimine increases Km and slightly decreases Vmax
8-BromoNAD+
-
-
8-oxo-dGDP
-
the ADP-ribose cleavage is competitively inhibited by 8-oxo-dGDP (68% relative cleavage efficiency at 0.01 mM)
8-oxo-dGMP
-
the ADP-ribose cleavage is competitively inhibited by 8-oxo-dGMP (89% relative cleavage efficiency at 0.01 mM)
ADP
-
potent noncompetitive inhibitor
ADP-ribose
-
the 8-oxo-dGDP cleavage is competitively inhibited by ADP-ribose (22% relative cleavage efficiency at 0.005 mM)
fluoride
Mn2+
-
above 0.05 mM
N-acetyl-p-benzoquinoneimine
nitroprusside
thionicotinamideNAD+
-
-
additional information
-
no inhibitory effect is observed with 8-oxo-dGMP
-
top print hide
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
nitric oxide
-
NO stimulates non-enzymatic ADP-ribosylation, at cysteine residues in the presence of reductant, of NUDT5 using ADP-ribose and consequently activates its ADPRase activity. ADPRase activity in J774 macrophage cells is increased by the treatment with SNP, an exogenous NO generator, or TNF-alpha/IFN-gamma, endogenous NO inducers. NO has a regulatory role, overview
top print hide
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.045
2''-O-acetyl-ADP-ribose
-
at pH 7.5 and 37°C
-
0.76 - 7.6
2',3'-cAMP
0.0035 - 0.0038
8-oxo-dGDP
2.65 - 19
ADP
0.0209 - 0.3213
ADP-D-ribose
3.16
ADP-glucose
-
25°C, pH 7.6, wild-type enzyme
0.083 - 0.154
ADP-mannose
0.0019 - 2.1
ADP-ribose
0.0004 - 0.37
ADPribose
0.46
ADPribose 2'-phosphate
-
-
0.19 - 0.78
cADP-ribose
0.35 - 43
CDP-choline
3.9 - 31
CDP-ethanolamine
2 - 6.3
CDP-glycerol
1.36
CDP-ribose
-
25°C, pH 7.6, wild-type enzyme
0.3 - 0.33
FAD
1.1
GDP-ribose
-
25°C, pH 7.6, wild-type enzyme
additional information
additional information
-
top print hide
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.78
2''-O-acetyl-ADP-ribose
-
at pH 7.5 and 37°C
-
0.11 - 83
2',3'-cAMP
0.2 - 1.8
ADP
0.0019 - 13.7
ADP-D-ribose
9.1
ADP-glucose
-
25°C, pH 7.6, wild-type enzyme
0.00011 - 97
ADP-ribose
1.8 - 117
ADPribose
1.14
ADPribose 2'-phosphate
-
-
0.0005 - 16
cADP-ribose
0.025 - 79
CDP-choline
2.1 - 125.2
CDP-ethanolamine
0.8 - 95.6
CDP-glycerol
3.36
CDP-ribose
-
25°C, pH 7.6, wild-type enzyme
2.5 - 5
FAD
3.57
GDP-ribose
-
25°C, pH 7.6, wild-type enzyme
additional information
ADP-ribose
-
25°C, pH 7.6, mutant enzyme I19A
top print hide
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
17.3
2''-O-acetyl-ADP-ribose
-
at pH 7.5 and 37°C
-
0.1 - 32
2',3'-cAMP
0.0011 - 0.66
ADP
0.0027 - 630
ADP-D-ribose
0.03 - 1000
ADP-ribose
0.0001 - 44
cADP-ribose
0.002 - 180
CDP-choline
0.007 - 32
CDP-ethanolamine
0.12 - 48
CDP-glycerol
top print hide
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.015 - 0.15
fluoride
top print hide
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.02
F-
Homo sapiens
-
IC50: 0.02 mM
top print hide
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.439
-
ADPRibase I
8.59
-
-
12.81
-
ADPRibase II
18.2
-
ADPRibase-Mn
top print hide
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 9
-
activity at pH 8.0 is about 90% of the activity at pH 6.5 and at pH 9.0, activity with ADP-ribose
7 - 9
-
for cleavage of ADP-ribose
7 - 9
-
ADPRibase I and ADPRibase II
7.4 - 9
-
with 2.5-5 mM Mg2+ or 0.1-0.25 mM Mn2+
10
-
for cleavage of 8-oxo-dGDP
top print hide
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5 - 10
-
pH 4.5: about 55% of maximal activity, pH 10.0: about 50% of maximal activity, activity with ADP-mannose
6 - 10
-
pH 6.0: about 25% of maximal activity, pH 10.0: about 60% of maximal activity, activity with ADP-ribose
7 - 9
-
linearly decreasing activity profile from pH 7 to pH 9, with activity at pH 9 being 50% of that at pH 7
7.5 - 10
-
pH 7.5: about 60% of maximal activity with ADP-ribose, about 50% of maximal activity with ADP-mannose, pH 10.0: about 70% of maximal activity with activity with ADP-ribose or ADP-mannose
8 - 10
pH 8.0: about 40% of maximal activity, pH 10.0: about 60% of maximal activity
top print hide
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
top print hide
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37 - 75
-
rate of hydrolysis of ADPribose is 15fold higher than at 37°C, incubations at higher temperatures are impractical because of the spontaneous hydrolysis of the substrate
top print hide
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
top print hide
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
Raji and Daudi
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
-
activity in leaves is lower than in stem and root, AtNUDT10; activity in roots is lower than in leaves and stem, AtNUDT6; AtNUDT2; AtNUDT7
Manually annotated by BRENDA team
-
dermis and epidermis of the outer and the inner prepuce
Manually annotated by BRENDA team
-
activity in leaves is lower than in stem and root, AtNUDT10; activity in roots is lower than in leaves and stem, AtNUDT6; AtNUDT2; AtNUDT7
Manually annotated by BRENDA team
top print hide
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
top print hide
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)
Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)
Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
top print hide
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
21800
2 * 21800, calculated and gel filtration
24300
-
2 * 24300, native protein, mass spectrometry
26735
6 * 26735, calculation from nucleotide sequence
28000
6 * 28000, SDS-PAGE
31000
-
gel filtration
31600
deduced from amino acid sequence
34000
-
2 * 34000, SDS-PAGE with and without mercaptoethanol
35000
-
gel filtration
36000 - 37000
-
gel filtration
38000
-
gel filtration
39121
-
1 * 39121, calculation from nucleotide sequence
68000
-
gel filtration
85000
-
dimeric thioredoxin fusion protein expressed in Escherichia coli, gel filtration
166000
gel filtration
top print hide
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
6 * 26735, calculation from nucleotide sequence; 6 * 28000, SDS-PAGE
homodimer
-
-
monomer
-
1 * 39121, calculation from nucleotide sequence
additional information
top print hide
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
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
-
top print hide
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
80
-
5 min, retains full activity
85
-
5 min, 30% loss of activity
top print hide
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, no loss of activity after months
-
top print hide
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
acetaminophen-treated animals and controls; ADPribose pyrophosphatase I; partial
-
ADP-ribose pyrophosphatase Sll1054; ADP-ribose pyrophosphatase Slr0920; ADP-ribose pyrophosphatase Slr1134
-
ADPRibaseI, ADPribase II and ADPRibase-Mn
-
ammonium sulfate precipitation, Toyopearl Phenyl-650M column chromatography, and Q Sepharose column chromatography
-
AtNUDT10; AtNUDT2; AtNUDT6; AtNUDT7
-
Ni-NTA column chromatography and Q-Sepharose column chromatography
-
Ni-Sepharose 6 column chromatography, HisTrap column chromatography, and Superdex 75 gel filtration
-
partial
recombinant enzyme
recombinant GST-tagged enzyme from Escherichia coli by glutathione affinity chromatography, the tag is cleaved off by TEV protease, and the detagged protein is further purified by anion exchange chromatography
recombinant His-tagged enzyme from Escherichia coli strain Bl21 by nickel affinity and anion exchange chromatography, and gel filtration
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
-
recombinant His6-tagged NUDT5 from Escherichia coli strain BL21 by nickel affinity chromatography
-
recombinant Ndx2 from Escherichia coli strain BL21(DE3) by heat treatment at 70°C for 15 min and ion exchange chromatography
-
Talon resin column chromatography
-
top print hide
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
; overexpression of wild-type and mutant enzymes
-
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli M15 cells
-
expression as a thioredoxin fusion protein in Escherichia coli
-
expression in Escherichia coli
expression in Escherichia coli, ADP-ribose pyrophosphatase Sll1054; expression in Escherichia coli, ADP-ribose pyrophosphatase Slr0920; expression in Escherichia coli, ADP-ribose pyrophosphatase Slr1134
-
expression in Escherichia coli, AtNUDT10; expression in Escherichia coli, AtNUDT2; expression in Escherichia coli, AtNUDT6; expression in Escherichia coli, AtNUDT7
-
expression of GST-tagged nezyme in Escherichia coli
expression of Ndx2 in Escherichia coli strain BL21(DE3)
-
expression of ORF38 as His6-tagged protein in Escherichia coli strain Bl21(DE3)
-
expression of the His-tagged enzyme in Escherichia coli strain Bl21
gene NUDT5, expression in murine J774A.1 macrophage cells, expression of His6-tagged NUDT5 in Escherichia coli strain BL21
-
hexahistidine-tagged recombinant enzyme expressed in Escherichia coli
overproduction in Escherichia coli
-
top print hide
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
oxidative stress caused by 0.003 mM paraquat for 7 days causes an increase in the total ADP-ribose diphosphohydrolase activity of NUDX7
top print hide
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H97A
mutant shows 60fold decrease in activity for substrates ADP-ribose and ADP and 300–500fold for CDP-alcohols. For H97A, 2',3'-cAMP is a better substrate than ADP-ribose
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; the mutant shows reduced catalytic efficiency compared to the wild type enzyme
C253A
mutant displays a tenfold increased efficiency for cADP-ribose, with no or modest effect on the other substrates
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; the mutant shows reduced catalytic efficiency compared to the wild type enzyme
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; the mutant shows reduced catalytic efficiency compared to the wild type enzyme
D164A
-
the mutant shows reduced catalytic efficiency compared to the wild type enzyme
D164N
-
the mutant shows increased catalytic efficiency compared to the wild type enzyme
E112Q
-
the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme
E115Q
-
the mutant shows reduced catalytic efficiency compared to the wild type enzyme
E116Q
-
the mutant shows reduced catalytic efficiency compared to the wild type enzyme
E166Q
-
the mutant shows reduced catalytic efficiency compared to the wild type enzyme
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; the mutant shows reduced catalytic efficiency compared to the wild type enzyme
F210A
lowers 40-70fold the catalytic efficiency for ADP-ribose, CDP-choline and 2',3'-cAMP hydrolysis, and 500fold for cADP-ribose
F37A
19fold increased Km for ADP-ribose, with only a 2-3fold increase of the CDP-choline and 2',3'-cAMP Km values
F37A/L196A
mutation lessens the relative preference for ADP-ribose versus cADP-ribose
F37A/L196F
mutation lessens the relative preference for ADP-ribose versus cADP-ribose
F37A/L196F/C253A
cyclic ADP-ribose is the best substrate for the mutant
F37Y
similar kinetic parameters as the wild type
H111A
marked efficiency decrease with all substrates except 2',3'-cAMP
H111N
marked efficiency decrease with all substrates except 2',3'-cAMP
L196A
mutation causes only a modest 2-5fold decrease of catalytic efficiency with the four substrates tested