Literature summary for 3.6.1.13 extracted from

Wakamatsu, T.; Nakagawa, N.; Kuramitsu, S.; Masui, R.
Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8 (2008), J. Bacteriol., 190, 1108-1117.

Cloned(Commentary)

Cloned (Comment)	Organism
expression of Ndx2 in Escherichia coli strain BL21(DE3)	Thermus thermophilus

Crystallization (Commentary)

Crystallization (Comment)	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 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	Thermus thermophilus

Crystallization (Comment)

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 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

Thermus thermophilus

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.25	-	ADP-ribose	pH 9.0, 25°C	Thermus thermophilus
0.3	-	FAD	pH 7.5, 25°C	Thermus thermophilus
0.33	-	FAD	pH 9.0, 25°C	Thermus thermophilus
0.52	-	ADP-ribose	pH 7.5, 25°C	Thermus thermophilus

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	binding structure, overview	Thermus thermophilus

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
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	UniProt	Comment	Textmining
Thermus thermophilus	Q84CU3	-	-
Thermus thermophilus HB8 / ATCC 27634 / DSM 579	Q84CU3	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant Ndx2 from Escherichia coli strain BL21(DE3) by heat treatment at 70°C for 15 min and ion exchange chromatography	Thermus thermophilus

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
ADP-glucose + H2O	low activity	Thermus thermophilus	?	-	?
ADP-glucose + H2O	low activity	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	?	-	?
ADP-ribose + H2O	-	Thermus thermophilus	AMP + D-ribose 5-phosphate	-	?
ADP-ribose + H2O	preferred substrate, substrate recognition and binding structure, overview	Thermus thermophilus	AMP + D-ribose 5-phosphate	-	?
ADP-ribose + H2O	-	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	AMP + D-ribose 5-phosphate	-	?
ADP-ribose + H2O	preferred substrate, substrate recognition and binding structure, overview	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	AMP + D-ribose 5-phosphate	-	?
FAD + H2O	preferred substrate	Thermus thermophilus	?	-	?
FAD + H2O	preferred substrate	Thermus thermophilus HB8 / ATCC 27634 / DSM 579	?	-	?

Synonyms

Synonyms	Comment	Organism
ADPR pyrophosphatase	-	Thermus thermophilus
ADPRase	-	Thermus thermophilus
Ndx2	-	Thermus thermophilus

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
25	-	assay at	Thermus thermophilus

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
1.4	-	ADP-ribose	pH 7.5, 25°C	Thermus thermophilus
2.5	-	FAD	pH 7.5, 25°C	Thermus thermophilus
4.9	-	ADP-ribose	pH 9.0, 25°C	Thermus thermophilus
5	-	FAD	pH 9.0, 25°C	Thermus thermophilus

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
9	-	-	Thermus thermophilus

pH Range

pH Minimum	pH Maximum	Comment	Organism
7.5	9	-	Thermus thermophilus