Information on EC 3.6.1.53 - Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.6.1.53
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RECOMMENDED NAME
GeneOntology No.
Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate
show the reaction diagram
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CDP-choline + H2O = CMP + phosphocholine
show the reaction diagram
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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]. In rat, the enzyme is found predominantly in thymus and spleen.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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UniProt
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2',3'-cAMP + H2O
?
show the reaction diagram
adenosine 5'-diphospho-5'-adenosine + H2O
AMP
show the reaction diagram
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-
45% of the activity with ADP-ribose
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?
ADP + H2O
?
show the reaction diagram
27% activity at 0.5 mM substrate compared to ADP-ribose
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-
?
ADP + H2O
AMP + phosphate
show the reaction diagram
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
show the reaction diagram
CDP-choline + H2O
CMP + phosphocholine
show the reaction diagram
CDP-ethanolamine + H2O
?
show the reaction diagram
89% activity at 0.5 mM substrate compared to ADP-ribose
-
-
?
CDP-ethanolamine + H2O
CMP + phosphoethanolamine
show the reaction diagram
CDP-glycerol + H2O
?
show the reaction diagram
89% activity at 0.5 mM substrate compared to ADP-ribose
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-
?
CDP-glycerol + H2O
CMP + phosphoglycerol
show the reaction diagram
cyclic ADP-ribose + H2O
N1-(5-phosphoribosyl)-AMP
show the reaction diagram
cyclic ADP-ribose + H2O
N1-(5-phosphoribosyl)-AMP + ?
show the reaction diagram
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ADPRibase-Mn activity on cyclic ADP-ribose is 65fold less efficient than on ADP-ribose
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-
?
FAD + H2O
?
show the reaction diagram
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39% of the activity with ADP-ribose
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?
IDP-ribose + H2O
IMP + D-ribose 5-phosphate
show the reaction diagram
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105% of the activity with ADP-ribose
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?
NAD+ + H2O
?
show the reaction diagram
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23% of the activity with ADP-ribose
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?
NADH + H+ + H2O
?
show the reaction diagram
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25% of the activity with ADP-ribose
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?
additional information
?
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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-ribose + H2O
AMP + D-ribose 5-phosphate
show the reaction diagram
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best substrate
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-
?
cyclic ADP-ribose + H2O
N1-(5-phosphoribosyl)-AMP
show the reaction diagram
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cADPR is an ADPRibase-Mn ligand and substrate
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-
?
additional information
?
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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 hide
LITERATURE
Mg2+
about 25% of the activity with Mn2+
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
o-phenanthroline
5 mM causes near full inactivation in 1.5 h
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 hide
LITERATURE
IMAGE
0.76 - 7.6
2',3'-cAMP
0.201 - 19
ADP
0.015 - 2.1
ADP-ribose
0.3 - 43
CDP-choline
1.422 - 31
CDP-ethanolamine
0.304 - 6.3
CDP-glycerol
0.17 - 0.78
cyclic ADP-ribose
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.11 - 83
2',3'-cAMP
0.2 - 4.4
ADP
0.003 - 97
ADP-ribose
0.025 - 79
CDP-choline
2.1 - 125.2
CDP-ethanolamine
0.8 - 95.6
CDP-glycerol
0.005 - 16
cyclic ADP-ribose
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1 - 32
2',3'-cAMP
942
0.011 - 0.66
ADP
13
0.03 - 1000
ADP-ribose
402
0.006 - 180
CDP-choline
1216
0.07 - 32
CDP-ethanolamine
1604
0.12 - 48
CDP-glycerol
3020
0.0001 - 44
cyclic ADP-ribose
5708
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
18.2
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pH 7.5, 37°C
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
activity towards ADP- and CDP-alcohols
7.5 - 8.5
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assay at
8 - 8.5
; ADP-ribose hydrolase activity
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.6
half-maximum activity
9.2
half-maximum activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
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assay at
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.3
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isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
ADPRibase-Mn activity in spleen is 2.5-5fold higher than in liver and muscle
Manually annotated by BRENDA team
ADPRibase-Mn activity in thymus is 2.5-5fold higher than in liver and muscle
Manually annotated by BRENDA team
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30000
gel filtration
32000
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gel filtration
39360
calculated from amino acid sequence
40000
1 * 39360, calculated, 1 * 40000, SDS-PAGE, enzyme plus N-terminal extension GPLGSPNS left after proteolysis of recombinant fusion protein
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
1 * 30000, gel filtration; 1 * 39360, calculated, 1 * 40000, SDS-PAGE, enzyme plus N-terminal extension GPLGSPNS left after proteolysis of recombinant fusion protein
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
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homology modeling based on crystal structure of the Danio rerio protein, Protein Data Base entry 2NXF, and docking of ADP-ribose
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
the activities towards ADP and CDP-alcohols are highest at pH 6-8 and decrease abruptly at higher pH
690823
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 1 mM EDTA, stable for months
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
glutathione-Sepharose column chromatography; recombinant GSt-fusion protein, in-column proteolysis of fusion
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 cells; expression as GST-fusion protein
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H97A
severe reduction of activtiy
C253A
10fold increase of the catalytic efficiency for cyclic ADP-ribose; Cys253 is hindering for cADPR phosphohydrolase activity, specific tenfold gain of efficiency with cyclic ADP-ribose
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
Phe37 is needed for ADP-ribose preference without catalytic effect
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
cyclic ADP-ribose is the best substrate, with a 8fold increase in catalytic efficiency compared to wild-type
F37Y
kinetic parameters similar to wild-type
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