BRENDA - Enzyme Database
show all sequences of 3.6.1.13

Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8

Wakamatsu, T.; Nakagawa, N.; Kuramitsu, S.; Masui, R.; J. Bacteriol. 190, 1108-1117 (2008)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression of Ndx2 in Escherichia coli strain BL21(DE3)
Thermus thermophilus
Crystallization (Commentary)
Crystallization
Organism
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 20C, 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
Thermus thermophilus
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.25
-
ADP-ribose
pH 9.0, 25C
Thermus thermophilus
0.3
-
FAD
pH 7.5, 25C
Thermus thermophilus
0.33
-
FAD
pH 9.0, 25C
Thermus thermophilus
0.52
-
ADP-ribose
pH 7.5, 25C
Thermus thermophilus
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
binding structure, overview
Thermus thermophilus
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ADP-ribose + H2O
Thermus thermophilus
-
AMP + D-ribose 5-phosphate
-
-
?
ADP-ribose + H2O
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
AMP + D-ribose 5-phosphate
-
-
?
FAD + H2O
Thermus thermophilus
preferred substrate
?
-
-
?
FAD + H2O
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
preferred substrate
?
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Thermus thermophilus
Q84CU3
-
-
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Q84CU3
-
-
Purification (Commentary)
Commentary
Organism
recombinant Ndx2 from Escherichia coli strain BL21(DE3) by heat treatment at 70C for 15 min and ion exchange chromatography
Thermus thermophilus
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ADP-glucose + H2O
low activity
687404
Thermus thermophilus
?
-
-
-
?
ADP-glucose + H2O
low activity
687404
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
?
-
-
-
?
ADP-ribose + H2O
-
687404
Thermus thermophilus
AMP + D-ribose 5-phosphate
-
-
-
?
ADP-ribose + H2O
preferred substrate, substrate recognition and binding structure, overview
687404
Thermus thermophilus
AMP + D-ribose 5-phosphate
-
-
-
?
ADP-ribose + H2O
-
687404
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
AMP + D-ribose 5-phosphate
-
-
-
?
ADP-ribose + H2O
preferred substrate, substrate recognition and binding structure, overview
687404
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
AMP + D-ribose 5-phosphate
-
-
-
?
FAD + H2O
preferred substrate
687404
Thermus thermophilus
?
-
-
-
?
FAD + H2O
preferred substrate
687404
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
?
-
-
-
?
Temperature Optimum [C]
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
25
-
assay at
Thermus thermophilus
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.4
-
ADP-ribose
pH 7.5, 25C
Thermus thermophilus
2.5
-
FAD
pH 7.5, 25C
Thermus thermophilus
4.9
-
ADP-ribose
pH 9.0, 25C
Thermus thermophilus
5
-
FAD
pH 9.0, 25C
Thermus thermophilus
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9
-
-
Thermus thermophilus
pH Range
pH Minimum
pH Maximum
Commentary
Organism
7.5
9
-
Thermus thermophilus
Cloned(Commentary) (protein specific)
Commentary
Organism
expression of Ndx2 in Escherichia coli strain BL21(DE3)
Thermus thermophilus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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 20C, 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
Thermus thermophilus
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.25
-
ADP-ribose
pH 9.0, 25C
Thermus thermophilus
0.3
-
FAD
pH 7.5, 25C
Thermus thermophilus
0.33
-
FAD
pH 9.0, 25C
Thermus thermophilus
0.52
-
ADP-ribose
pH 7.5, 25C
Thermus thermophilus
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
binding structure, overview
Thermus thermophilus
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ADP-ribose + H2O
Thermus thermophilus
-
AMP + D-ribose 5-phosphate
-
-
?
ADP-ribose + H2O
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
AMP + D-ribose 5-phosphate
-
-
?
FAD + H2O
Thermus thermophilus
preferred substrate
?
-
-
?
FAD + H2O
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
preferred substrate
?
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant Ndx2 from Escherichia coli strain BL21(DE3) by heat treatment at 70C for 15 min and ion exchange chromatography
Thermus thermophilus
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ADP-glucose + H2O
low activity
687404
Thermus thermophilus
?
-
-
-
?
ADP-glucose + H2O
low activity
687404
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
?
-
-
-
?
ADP-ribose + H2O
-
687404
Thermus thermophilus
AMP + D-ribose 5-phosphate
-
-
-
?
ADP-ribose + H2O
preferred substrate, substrate recognition and binding structure, overview
687404
Thermus thermophilus
AMP + D-ribose 5-phosphate
-
-
-
?
ADP-ribose + H2O
-
687404
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
AMP + D-ribose 5-phosphate
-
-
-
?
ADP-ribose + H2O
preferred substrate, substrate recognition and binding structure, overview
687404
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
AMP + D-ribose 5-phosphate
-
-
-
?
FAD + H2O
preferred substrate
687404
Thermus thermophilus
?
-
-
-
?
FAD + H2O
preferred substrate
687404
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
?
-
-
-
?
Temperature Optimum [C] (protein specific)
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
25
-
assay at
Thermus thermophilus
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
1.4
-
ADP-ribose
pH 7.5, 25C
Thermus thermophilus
2.5
-
FAD
pH 7.5, 25C
Thermus thermophilus
4.9
-
ADP-ribose
pH 9.0, 25C
Thermus thermophilus
5
-
FAD
pH 9.0, 25C
Thermus thermophilus
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9
-
-
Thermus thermophilus
pH Range (protein specific)
pH Minimum
pH Maximum
Commentary
Organism
7.5
9
-
Thermus thermophilus
Other publictions for EC 3.6.1.13
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
735009
Cabezas
Molecular bases of catalysis a ...
Homo sapiens
PLoS ONE
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-
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1
13
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42
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7
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4
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44
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1
13
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42
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4
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44
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54
54
734285
Karuppiah
Structure and mechanism of the ...
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J. Biol. Chem.
289
33187-33197
2014
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1
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4
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718517
Okazaki
Crystallization and preliminar ...
Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Acta Crystallogr. Sect. F
68
49-52
2012
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1
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735057
Rodrigues
Characterization of Danio reri ...
Danio rerio
PLoS ONE
7
e42249
2012
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1
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13
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8
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13
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13
13
715407
Ito
Cleavage of oxidized guanine n ...
Homo sapiens
J. Biochem.
149
731-738
2011
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1
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5
4
-
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3
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1
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1
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3
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2
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741073
Arimori
Diverse substrate recognition ...
Homo sapiens
Nucleic Acids Res.
39
8972-8983
2011
-
-
1
1
-
-
-
-
-
1
-
1
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2
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1
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3
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1
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1
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1
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1
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3
-
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720769
Ishikawa
Distinct regulation of Arabido ...
Arabidopsis thaliana
Plant Signal. Behav.
5
839-841
2010
-
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1
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1
1
1
1
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700755
Ogawa
Overexpression of an ADP-ribos ...
Arabidopsis thaliana
Plant J.
57
289-301
2009
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710725
Goncalves
Structure of an N-terminally t ...
Deinococcus radiodurans
Acta Crystallogr. Sect. F
65
1083-1087
2009
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1
1
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2
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1
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1
-
-
-
-
-
-
687404
Wakamatsu
Structural basis for different ...
Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579
J. Bacteriol.
190
1108-1117
2008
-
-
1
1
-
-
-
4
-
1
-
4
-
6
-
-
1
-
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8
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1
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4
1
1
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1
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1
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1
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1
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8
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1
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4
1
1
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688413
Zha
Molecular mechanism of ADP-rib ...
Homo sapiens
J. Mol. Biol.
379
568-578
2008
-
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1
1
20
-
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22
1
1
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1
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4
1
1
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21
1
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2
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2
30
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22
1
1
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2
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1
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4
1
1
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21
1
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20
20
690090
Huang
Bifunctional NMN adenylyltrans ...
Francisella tularensis, Synechocystis sp.
Structure
16
196-209
2008
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2
2
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6
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684834
Yu
Activation of NUDT5, an ADP-ri ...
Homo sapiens
Biochem. Biophys. Res. Commun.
354
764-768
2007
1
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1
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690189
Ge
AcMNPV ORF38 protein has the a ...
Autographa californica multiple nucleopolyhedrovirus
Virology
361
204-211
2007
-
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1
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1
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1
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1
1
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667823
Carloto
The specific, submicromolar-K( ...
Homo sapiens
Biochim. Biophys. Acta
1760
1545-1551
2006
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2
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1
1
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670632
Jambunathan
Analysis of Arabidopsis growth ...
Arabidopsis sp.
Planta
224
1-11
2006
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