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Information on EC 3.6.1.13 - ADP-ribose diphosphatase

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EC Tree
     3 Hydrolases
         3.6 Acting on acid anhydrides
             3.6.1 In phosphorus-containing anhydrides
                3.6.1.13 ADP-ribose diphosphatase
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UNIPROT: Q84CU3 not found.
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The enzyme appears in viruses and cellular organisms
Synonyms
nudt5, nudt9, adp-ribose pyrophosphatase, adprase, atnudt7, adpribase-mn, atnudx7, adp-ribose hydrolase, nudt5 protein, adpr pyrophosphatase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ADP-ribose pyrophosphatase
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ADP-ribose pyrophosphatase-I
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ADPR pyrophosphatase
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adenosine diphosphoribose pyrophosphatase
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ADP-ribose diphosphatase
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ADP-ribose phosphohydrolase
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-
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ADP-ribose pyrophosphatase
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-
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ADPR-PPase
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ADPRibase
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ADPribose pyrophosphatase
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pyrophosphatase, adenosine diphosphoribose
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphorous acid anhydride hydrolysis
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-
-
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PATHWAY SOURCE
PATHWAYS
SYSTEMATIC NAME
IUBMB Comments
ADP-D-ribose ribophosphohydrolase
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CAS REGISTRY NUMBER
COMMENTARY hide
9024-83-3
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ADP-glucose + H2O
?
show the reaction diagram
low activity
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-
?
ADP-ribose + H2O
AMP + D-ribose 5-phosphate
show the reaction diagram
FAD + H2O
?
show the reaction diagram
preferred substrate
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
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
-
-
-
?
FAD + H2O
?
show the reaction diagram
preferred substrate
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
the ADP-ribose pyrophosphatase reaction in crystalline state is conducted by consecutive binding of two Mn(II) ions as cofactors. Two Mn2+ ions are inserted consecutively into the catalytic center of the ES-state and ligated by Glu86 and Glu82, which are highly conserved among the Nudix family, in the ESM- and ESMM-states
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.25 - 0.52
ADP-ribose
0.3 - 0.33
FAD
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.4 - 8
ADP-ribose
2.5 - 5
FAD
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
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SwissProt
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
adenosine diphosphate ribose pyrophosphatase (ADPRase) is a member of the Nudix family
physiological function
TtADPRase catalyzes the metal-induced and concerted general acid-base hydrolysis of ADP ribose (ADPR) into AMP and ribose-5'-phosphate (R5P)
additional information
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
Q84CU3_THETH
170
0
19264
TrEMBL
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
38000
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, Toyopearl Phenyl-650M column chromatography, and Q Sepharose column chromatography
recombinant Ndx2 from Escherichia coli strain BL21(DE3) by heat treatment at 70°C for 15 min and ion exchange chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expression of Ndx2 in Escherichia coli strain BL21(DE3)
overproduction in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Yoshiba, S.; Nakagawa, N.; Masui, R.; Shibata, T.; Inoue, Y.; Yokoyama, S.; Kuramitsu, S.
Overproduction, crystallization and preliminary diffraction data of ADP-ribose pyrophosphatase from Thermus thermophilus HB8
Acta Crystallogr. Sect. D
59
1840-1842
2003
Thermus thermophilus (Q84CU3), Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (Q84CU3)
Manually annotated by BRENDA team
Wakamatsu, T.; Nakagawa, N.; Kuramitsu, S.; Masui, R.
Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8
J. Bacteriol.
190
1108-1117
2008
Thermus thermophilus (Q84CU3), Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (Q84CU3)
Manually annotated by BRENDA team
Okazaki, N.; Adachi, M.; Tamada, T.; Kurihara, K.; Ooga, T.; Kamiya, N.; Kuramitsu, S.; Kuroki, R.
Crystallization and preliminary neutron diffraction studies of ADP-ribose pyrophosphatase-I from Thermus thermophilus HB8
Acta Crystallogr. Sect. F
68
49-52
2012
Thermus thermophilus (Q84CU3), Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (Q84CU3)
Manually annotated by BRENDA team
Furuike, Y.; Akita, Y.; Miyahara, I.; Kamiya, N.
ADP-ribose pyrophosphatase reaction in crystalline state conducted by consecutive binding of two manganese (II) ions as cofactors
Biochemistry
55
1801-1812
2016
Escherichia coli (Q93K97), Homo sapiens (Q9UKK9), Mycobacterium tuberculosis (O33199), Mycobacterium tuberculosis CDC 1551 (O33199), Mycobacterium tuberculosis Oshkosh (O33199), Thermus thermophilus, Thermus thermophilus (Q84CU3)
Manually annotated by BRENDA team