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Information on EC 3.6.1.53 - Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase
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3.6.1.53 Mn2+-dependent ADP-ribose/CDP-alcohol diphosphataseIUBMB Comments
Requires Mn2+. Unlike EC 3.6.1.13, ADP-ribose diphosphatase, it cannot utilize Mg2+. ADP-D-ribose, CDP-choline, CDP-ethanolamine and ADP are substrates for this enzyme but ADP-D-glucose, UDP-D-glucose, CDP-D-glucose, CDP, CMP and AMP are not hydrolysed . The mammalian enzyme hydrolyses cyclic ADP-ribose to 1-(5-phospho-beta-D-ribosyl)-AMP with ~100-fold lower efficiency than ADP-D-ribose . In rat, the enzyme is found predominantly in thymus and spleen.
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Word Map
- 3.6.1.53
- dithiothreitol
-
adp-ribosylation
-
nonenzymatic
-
hepatotoxicity
- nitroprusside
-
cadpr
- rodent
- n-acetyl-p-benzoquinoneimine
-
napqi
-
cdp-alcohols
-
phosphohydrolysis
- acetaminophen
- pyrophosphatases
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Reaction Schemes
Synonyms
ADP-ribose/CDP-alcohol diphosphatase, ADPRibase-I, ADPRibase-II, ADPRibase-Mn, Adprm, cADPR phosphohydrolase, Mn(2+)-dependent ADP-ribose/CDP-alcohol pyrophosphatase, Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase, More, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
ADPRibase-Mn
Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase
ADPRibase-Mn
-
-
-
-
Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
-
-
-
-
CDP-choline + H2O = CMP + phosphocholine
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
CDP-choline phosphohydrolase
Requires Mn2+. Unlike EC 3.6.1.13, ADP-ribose diphosphatase, it cannot utilize Mg2+. ADP-D-ribose, CDP-choline, CDP-ethanolamine and ADP are substrates for this enzyme but ADP-D-glucose, UDP-D-glucose, CDP-D-glucose, CDP, CMP and AMP are not hydrolysed [2]. The mammalian enzyme hydrolyses cyclic ADP-ribose to 1-(5-phospho-beta-D-ribosyl)-AMP with ~100-fold lower efficiency than ADP-D-ribose [3]. In rat, the enzyme is found predominantly in thymus and spleen.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
adenosine 5'-diphospho-5'-adenosine + H2O
AMP
-
-
45% of the activity with ADP-ribose
-
?
ADP + H2O
?
27% activity at 0.5 mM substrate compared to ADP-ribose
-
-
?
CDP-ethanolamine + H2O
?
89% activity at 0.5 mM substrate compared to ADP-ribose
-
-
?
CDP-glycerol + H2O
?
89% activity at 0.5 mM substrate compared to ADP-ribose
-
-
?
IDP-ribose + H2O
IMP + D-ribose 5-phosphate
-
-
105% of the activity with ADP-ribose
-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
100% activity at 0.5 mM substrate
-
-
?
CDP-choline + H2O
CMP + phosphocholine
-
140% of the activity with ADP-ribose
-
-
?
CDP-choline + H2O
CMP + phosphocholine
156% of the activity with ADP-ribose
-
-
?
CDP-choline + H2O
CMP + phosphocholine
140% activity at 0.5 mM substrate compared to ADP-ribose
-
-
?
CDP-ethanolamine + H2O
CMP + phosphoethanolamine
84% of the activity with ADP-ribose
-
-
?
CDP-ethanolamine + H2O
CMP + phosphoethanolamine
-
89% of the activity with ADP-ribose
-
-
?
CDP-glycerol + H2O
CMP + phosphoglycerol
103% of the activity with ADP-ribose
-
-
?
CDP-glycerol + H2O
CMP + phosphoglycerol
-
89% of the activity with ADP-ribose
-
-
?
cyclic ADP-ribose + H2O
N1-(5-phosphoribosyl)-AMP
-
cADPR is an ADPRibase-Mn ligand and substrate
-
-
?
cyclic ADP-ribose + H2O
N1-(5-phosphoribosyl)-AMP
-
ADPRibase-Mn activity on cyclic ADP-ribose is 65fold less efficient than on ADP-ribose
-
-
?
cyclic ADP-ribose + H2O
N1-(5-phosphoribosyl)-AMP
-
product determination and analysis, cADPR is an ADPRibase-Mn ligand and substrate. ADPRibase-Mn activity on cADPR is 65fold less efficient than on ADP-ribose, the best substrate. Phosphohydrolytic pattern of the reaction, overview
-
-
?
additional information
?
-
very poor substrate: cyclic ADP-ribose. No substrate: ADP-glucose, UDP-glucose, CDP-glucose, CDP, CMP, AMP or 3',5'-cAMP
-
-
?
additional information
?
-
ADP-ribose/CDP-alcohol diphosphatase (ADPRibase-Mn) acts as cyclic ADP-ribose (cADPR) phosphohydrolase with much lower efficiency than on its major substrates
-
-
-
additional information
?
-
-
ADPRibase-Mn hydrolyzes the phosphoanhydride linkages of ADP-ribose, CDP-choline, CDP-glycerol, CDP-ethanolamine, and ADP with decreasing efficiencies, requiring low micromolar Mn2+ concentrations not substituted by Mg2+. ADPRibase-Mn hydrolyzes ADP-ribose, CDP-choline, CDP-glycerol and CDP-ethanolamine with decreasing catalytic efficiencies
-
-
?
additional information
?
-
ADP-glucose, UDP-glucose, CDP-glucose, CDP, CMP, and AMP are not hydrolysed
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
cyclic ADP-ribose + H2O
N1-(5-phosphoribosyl)-AMP
-
cADPR is an ADPRibase-Mn ligand and substrate
-
-
?
additional information
?
-
ADP-ribose/CDP-alcohol diphosphatase (ADPRibase-Mn) acts as cyclic ADP-ribose (cADPR) phosphohydrolase with much lower efficiency than on its major substrates
-
-
-
additional information
?
-
-
ADPRibase-Mn hydrolyzes the phosphoanhydride linkages of ADP-ribose, CDP-choline, CDP-glycerol, CDP-ethanolamine, and ADP with decreasing efficiencies, requiring low micromolar Mn2+ concentrations not substituted by Mg2+. ADPRibase-Mn hydrolyzes ADP-ribose, CDP-choline, CDP-glycerol and CDP-ethanolamine with decreasing catalytic efficiencies
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mn2+
additional information
Mn2+
required, similar activatory effects with all the substrates tested. Km values around 1 microM and 2.5 mM Mn2+ for ADP-ribose hydrolysis
Mn2+
required. Concentration of MnCl2 giving the half-maximal rate is 0.001-0.004 mM. Mn2+ cannot be replaced by Mg2+
Mn2+
dependent on, ADPRibase-Mn is inactive without added Mn2+, and it shows a high affinity for the cation, since saturation is observed at low-micromolar concentrations of Mn2+ well below the substrate concentration (0.5 mM), in no case can Mg2+ replace Mn2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
incubation with 2.5 mM EDTA does not affect ADPRibase-Mn activity; not inhibitory: EDTA up to 2.5 mM
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.76
2',3'-cAMP
wild-type, pH 7.5, temperature not specified in the publication
1.7
2',3'-cAMP
mutant H97A, pH 7.5, temperature not specified in the publication
0.201
ADP
recombinant enzyme, in 50 mM Tris-HCl (pH 7.5), 0.1 mM MnCl2, at 37°C
0.039
ADP-ribose
recombinant enzyme, in 50 mM Tris-HCl (pH 7.5), 0.1 mM MnCl2, at 37°C
0.053
ADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
0.071
ADP-ribose
mutant H97A, pH 7.5, temperature not specified in the publication
0.3
CDP-choline
recombinant, in 50 mM Tris-HCl (pH 7.5), 0.1 mM MnCl2, at 37°C
12
CDP-choline
wild-type, pH 7.5, temperature not specified in the publication
43
CDP-choline
mutant H97A, pH 7.5, temperature not specified in the publication
1.422
CDP-ethanolamine
recombinant enzyme, in 50 mM Tris-HCl (pH 7.5), 0.1 mM MnCl2, at 37°C
3.9
CDP-ethanolamine
wild-type, pH 7.5, temperature not specified in the publication
31
CDP-ethanolamine
mutant H97A, pH 7.5, temperature not specified in the publication
0.304
CDP-glycerol
recombinant enzyme, in 50 mM Tris-HCl (pH 7.5), 0.1 mM MnCl2, at 37°C
2
CDP-glycerol
wild-type, pH 7.5, temperature not specified in the publication
6.3
CDP-glycerol
mutant H97A, pH 7.5, temperature not specified in the publication
0.19
cyclic ADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
16.9
2',3'-cAMP
wild-type, pH 7.5, temperature not specified in the publication
29.7
2',3'-cAMP
mutant H97A, pH 7.5, temperature not specified in the publication
4.4
ADP
recombinant enzyme, in 50 mM Tris-HCl (pH 7.5), 0.1 mM MnCl2, at 37°C
0.4
ADP-ribose
mutant H97A, pH 7.5, temperature not specified in the publication
12.8
ADP-ribose
recombinant enzyme, in 50 mM Tris-HCl (pH 7.5), 01 mM MnCl2, at 37°C
18
ADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
0.8
CDP-choline
mutant H97A, pH 7.5, temperature not specified in the publication
28.5
CDP-choline
recombinant enzyme, in 50 mM Tris-HCl (pH 7.5), 0.1 mM MnCl2, at 37°C
67.2
CDP-choline
wild-type, pH 7.5, temperature not specified in the publication
2.1
CDP-ethanolamine
mutant H97A, pH 7.5, temperature not specified in the publication
41.3
CDP-ethanolamine
recombinant enzyme, in 50 mM Tris-HCl (pH 7.5), 0.1 mM MnCl2, at 37°C
125.2
CDP-ethanolamine
wild-type, pH 7.5, temperature not specified in the publication
0.8
CDP-glycerol
mutant H97A, pH 7.5, temperature not specified in the publication
28.1
CDP-glycerol
recombinant enzyme, in 50 mM Tris-HCl (pH 7.5), 0.1 mM MnCl2, at 37°C
95.6
CDP-glycerol
wild-type, pH 7.5, temperature not specified in the publication
0.005
cyclic ADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
18
2',3'-cAMP
mutant H97A, pH 7.5, temperature not specified in the publication
22
2',3'-cAMP
wild-type, pH 7.5, temperature not specified in the publication
0.011
ADP
mutant H97A, pH 7.5, temperature not specified in the publication
5.9
ADP-ribose
mutant H97A, pH 7.5, temperature not specified in the publication
340
ADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
0.02
CDP-choline
mutant H97A, pH 7.5, temperature not specified in the publication
5.6
CDP-choline
wild-type, pH 7.5, temperature not specified in the publication
0.07
CDP-ethanolamine
mutant H97A, pH 7.5, temperature not specified in the publication
32
CDP-ethanolamine
wild-type, pH 7.5, temperature not specified in the publication
0.12
CDP-glycerol
mutant H97A, pH 7.5, temperature not specified in the publication
48
CDP-glycerol
wild-type, pH 7.5, temperature not specified in the publication
0.028
cyclic ADP-ribose
wild-type, pH 7.5, temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8 - 8.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
bifunctional Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
ADPRibase-Mn activity in spleen is 2.5-5fold higher than in liver and muscle
brenda
ADPRibase-Mn activity in thymus is 2.5-5fold higher than in liver and muscle
brenda
additional information
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
ADPRibase-Mn enzymes contain the dinuclear metal centre typical of the metallo-dependent phosphatases SCOP2 superfamily, forming within it a family of their own named as ADPRibase-Mn-like. ADPRibase-Mn proteins constitute also a functional family in the CATH classification, within cluster SC:3 of superfamily 3.60.21.10
physiological function
cyclic ADP-ribose (cADPR) is a messenger for Ca2+ mobilization. Its turnover is believed to occur by glycohydrolysis to ADP-ribose. ADP-ribose/CDP-alcohol diphosphatase (ADPRibase-Mn) acts as cADPR phosphohydrolase with much lower efficiency than on its major substrates
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40000
1 * 39360, calculated, 1 * 40000, SDS-PAGE, enzyme plus N-terminal extension GPLGSPNS left after proteolysis of recombinant fusion protein
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
monomer
1 * 39360, calculated, 1 * 40000, SDS-PAGE, enzyme plus N-terminal extension GPLGSPNS left after proteolysis of recombinant fusion protein
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
substrate-docking studies 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
substrate docking on a homology model of human ADPRibase-Mn suggests possible interactions of ADP-ribose with residue Cys253, within the metallo-dependent phosphatases signature with Gln27, Asn110, His111, or in unique structural regions of the ADPRibase-Mn family, residues Phe37 and Arg43 and Phe210
coordinates of rat ADPRibase-Mn, modelled by homology to the X-ray structure of its zebrafish orthologue, taken from the SWISS-MODEL repository, accession code q5m88. cADPR docking to a model of ADPRibase-Mn and molecular dynamics simulation, ADPRibase-Mn complexes with docked ligands show the active center in a closed conformation, overview
-
homology modeling based on crystal structure of the Danio rerio protein, Protein Data Base entry 2NXF, and docking of ADP-ribose
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C253A
F210A
mutation lowers 40-70fold the catalytic efficiency for ADP-ribose, CDP-choline and 2',3'-cAMP hydrolysis, and 500fold for cyclic ADP-ribose
F37A/L196A
modest enhancement of the inhibitory effect over that of the F37A point mutation
F37A/L196F
modest enhancement of the inhibitory effect over that of the F37A point mutation
F37A/L196F/C253A
F37A/L196F/C253G
site-directed mutagenesis, the mutant with a smaller residue 253 shows increased cADPR specificity
F37A/L196F/D250A/C253G
site-directed mutagenesis, the quadruple mutant shows a detrimental effect of the D250A substitution on the efficiency with all substrates (1.3-3.4fold decrease), and more markedly so for cADPR, such that the substrate efficiency ratios are less favourable than for the triple mutant F37A/ L196F/C253G
F37A/L196F/V252A/C253G
H111A
marked decrease in efficiency with all substrates except 2',3'-cAMP
H111N
marked decrease in efficiency with all substrates except 2',3'-cAMP
L196A
modest 2-5fold decrease of catalytic efficiency with the substrates tested
N110A
reduction of catalytic efficiency is stronger for the hydrolysis of CDP-choline or 2',3'-cAMP than for the hydrolysis of ADP-ribose or cADPR. The decrease of kcat value is stronger for the hydrolysis of 2',3'-cAMP
Q27H
for ADP-ribose, modest negative effects of similar magnitude in catalysis and in substrate binding. For CDP-choline, the substitution affects only binding. For 2',3'-cAMP, the substitution affects catalysis, not binding
R43A
Arg43 is essential for catalysis, drastic efficiency loss of the mutant
additional information
design of mutations at or near residue 253 of human ADPRibase-Mn, in the vicinity of the adenine N1-linked (northern) ribose of cADPR, for altering the substrate specificity of the enzyme, overview
C253A
Cys253 is hindering for cADPR phosphohydrolase activity, specific tenfold gain of efficiency with cyclic ADP-ribose
F37A/L196F/C253A
cyclic ADP-ribose is the best substrate, with a 8fold increase in catalytic efficiency compared to wild-type
F37A/L196F/C253A
site-directed mutagenesis, specific cyclic ADP-ribose phosphohydrolase obtained by mutagenic engineering of Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase. Mutagenesis of human ADPRibase-Mn at Phe37, Leu196 and Cys253 alters its specificity, the best substrate of the mutant is cyclic ADP-ribose (cADPR), the Cys253 mutation is essential for cADPR preference. The proximity to the northern ribose of cADPR in docking models indicates Cys253 is a steric constraint for cADPR positioning
F37A/L196F/V252A/C253G
site-directed mutagenesis, the mutant with displays the desired specificity, with cADPR kcat/KM is about 20-200fold larger than for any other substrate
F37A/L196F/V252A/C253G
site-directed mutagenesis, the quadruple mutant shows detrimental effects of the V252A substitution on the efficiency with ADP-ribose, CDP-choline and 2',3'-cAMP (1.1-2.8fold decrease) while it increases 2fold the efficiency with cADPR. F37A/L196F/V252A/C253G-ADPRibase-Mn displays substrate efficiency ratios highly
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 8
the activities towards ADP and CDP-alcohols are highest at pH 6-8 and decrease abruptly at higher pH
690823
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant GST-tagged wild-type and mutant enzymes from Escherichia coli strain BL21 by glutathione affinity chromatography, proteolytic tag cleavage
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene ADPRM, cloned from liver, recombinant expression of GST-tagged wild-type and mutant enzymes in Escherichia coli strain BL21
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Canales, J.; Pinto, R.M.; Costas, M.J.; Hernandez, M.T.; Miro, A.; Bernet, D.; Fernandez, A.; Cameselle, J.C.
Rat liver nucleoside diphosphosugar or diphosphoalcohol pyrophosphatase different from nucleotide pyrophosphatase or phosphodiesterase I: substrate specificities of Mg2+- and/or Mn2+-depeneent hydrolases acting on ADP-ribose
Biochim. Biophys. Acta
1246
167-177
1995
Rattus norvegicus
brenda
Canales, J.; Fernandez, A.; Ribeiro, J.M.; Cabezas, A.; Rodrigues, J.R.; Cameselle, J.C.; Costas, M.J.
Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase: a novel metallophosphoesterase family preferentially expressed in rodent immune cells
Biochem. J.
413
103-113
2008
Rattus norvegicus (Q5M886), Mus musculus (Q99KS6), Mus musculus
brenda
Canales, J.; Fernandez, A.; Rodrigues, J.R.; Ferreira, R.; Ribeiro, J.M.; Cabezas, A.; Costas, M.J.; Cameselle, J.C.
Hydrolysis of the phosphoanhydride linkage of cyclic ADP-ribose by the Mn(2+)-dependent ADP-ribose/CDP-alcohol pyrophosphatase
FEBS Lett.
583
1593-1598
2009
Rattus norvegicus
brenda
Cabezas, A.; Ribeiro, J.; Rodrigues, J.; Lopez-Villamizar, I.; Fernandez, A.; Canales, J.; Pinto, R.; Costas, M.; Cameselle, J.
Molecular bases of catalysis and ADP-ribose preference of human Mn2+-dependent adpribose/CDP-alcohol diphosphatase and conversion by mutagenesis to a preferential cyclic ADP-ribose phosphohydrolase
PLoS ONE
10
e0118680
2015
Homo sapiens (W0NWJ0), Homo sapiens
brenda
Rodrigues, J.; Fernandez, A.; Canales, J.; Cabezas, A.; Ribeiro, J.; Costas, M.; Cameselle, J.
Characterization of Danio rerio Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase, the structural prototype of the ADPRibase-Mn-like protein family
PLoS ONE
7
e42249
2012
Danio rerio (Q7T291)
brenda
Ribeiro, J.M.; Canales, J.; Cabezas, A.; Rodrigues, J.R.; Pinto, R.M.; Lopez-Villamizar, I.; Costas, M.J.; Cameselle, J.C.
Specific cyclic ADP-ribose phosphohydrolase obtained by mutagenic engineering of Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase
Sci. Rep.
8
1036
2018
Homo sapiens (Q3LIE5)
brenda
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