Literature summary for 3.1.3.82 extracted from

Nguyen, H.H.; Wang, L.; Huang, H.; Peisach, E.; Dunaway-Mariano, D.; Allen, K.N.
Structural determinants of substrate recognition in the HAD superfamily member D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) (2010), Biochemistry, 49, 1082-1092.

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Crystallization (Commentary)

Crystallization (Comment)	Organism
hanging-drop vapor-diffusion method, X-ray structures of the enzyme in a complex with Mg2+ and phosphate at 1.7 A resolution	Bordetella bronchiseptica
the X-ray crystallographic structures of Escherichia coli GmhB in the apo form (1.6 A resolution), in a complex with Mg2+ and orthophosphate (1.8 A resolution), and in a complex with Mg2+ and D-glycero-beta-D-manno-heptose 1,7-bisphosphate are determined	Escherichia coli

Protein Variants

Protein Variants	Comment	Organism
C107A	kcat/KM for D-glycero-beta-D-manno-heptose 1,7-bisphosphate is 875fold lower than wild-type value	Escherichia coli
C109A	kcat/KM for D-glycero-beta-D-manno-heptose 1,7-bisphosphate is 1400fold lower than wild-type value	Escherichia coli
C92A	kcat/KM for D-glycero-beta-D-manno-heptose 1,7-bisphosphate is 230fold lower than wild-type value	Escherichia coli
D13A	mutant is devoid of detectable activity toward the physiological substrate D-glycero-beta-D-manno-heptose 1,7-bisphosphate	Escherichia coli
K137A	kcat/KM for D-glycero-beta-D-manno-heptose 1,7-bisphosphate is 10fold lower than wild-type value	Escherichia coli
R110A	kcat/KM for D-glycero-beta-D-manno-heptose 1,7-bisphosphate is 230fold lower than wild-type value	Escherichia coli

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.005	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, wild-type	Escherichia coli
0.032	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C107A	Escherichia coli
0.039	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme K137A	Escherichia coli
0.045	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C109A	Escherichia coli
0.067	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, wild-type	Escherichia coli
0.068	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C109A	Escherichia coli
0.083	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C107A	Escherichia coli
0.18	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C92A	Escherichia coli
0.181	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme R110A	Escherichia coli
0.3	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C92A	Escherichia coli
0.68	-	D-fructose 1,6-bisphosphate	-	Bordetella bronchiseptica

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	contains Mg2+	Escherichia coli
Mg2+	enzyme contains Mg2+	Bordetella bronchiseptica
Zn2+	all four structures reveal a Zn2+ bound at the predicted Zn2+ binding loop as evidenced by strong X-ray fluorescence at the peak wavelength (Kedge) of Zn2+	Escherichia coli
Zn2+	GmhB possess a classical CxH-(x)nCxC motif that coordinates the Zn2+ with square planar geometry	Bordetella bronchiseptica

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
16000	-	gel filtration	Escherichia coli
20000	-	gel filtration	Bordetella bronchiseptica

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O	Escherichia coli	-	D-glycero-beta-D-manno-heptose 1-phosphate + phosphate	-	?
D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O	Bordetella bronchiseptica	-	D-glycero-beta-D-manno-heptose 1-phosphate + phosphate	-	?

Organism

Organism	UniProt	Comment	Textmining
Bordetella bronchiseptica	Q7WG29	-	-
Escherichia coli	P63228	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
D-fructose 1,6-bisphosphate + H2O	slow substrate	Bordetella bronchiseptica	?	-	?
D-glycero-alpha-D-manno-heptose 1,7-bisphosphate + H2O	kcat/Km for the beta-anomer is 100fold higher than for the alpha-anomer	Escherichia coli	D-glycero-alpha-D-manno-heptose 1-phosphate + phosphate	-	?
D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O	-	Escherichia coli	D-glycero-beta-D-manno-heptose 1-phosphate + phosphate	-	?
D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O	-	Bordetella bronchiseptica	D-glycero-beta-D-manno-heptose 1-phosphate + phosphate	-	?
D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O	kcat/Km for the beta-anomer is 100fold higher than for the alpha-anomer	Escherichia coli	D-glycero-beta-D-manno-heptose 1-phosphate + phosphate	-	?

Subunits

Subunits	Comment	Organism
monomer	1 * 16000, crystallographic data	Escherichia coli
monomer	1 * 20000, crystallographic data	Bordetella bronchiseptica

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.0017	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C92A	Escherichia coli
0.042	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C107A	Escherichia coli
0.057	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C109A	Escherichia coli
0.34	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C109A	Escherichia coli
0.55	-	D-fructose 1,6-bisphosphate	-	Bordetella bronchiseptica
0.63	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C107A	Escherichia coli
0.63	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C92A	Escherichia coli
2	8	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme K137A	Escherichia coli
4.6	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, wild-type	Escherichia coli
6.2	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme R110A	Escherichia coli
35.7	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, wild-type	Escherichia coli

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
0.006	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C92A	Escherichia coli
0.13	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C107A	Escherichia coli
1.3	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C109A	Escherichia coli
3.5	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C92A	Escherichia coli
5	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C109A	Escherichia coli
7.6	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme C107A	Escherichia coli
34.3	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme R110A	Escherichia coli
69	-	D-glycero-alpha-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, wild-type	Escherichia coli
718	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, mutant enzyme K137A	Escherichia coli
7140	-	D-glycero-beta-D-manno-heptose 1,7-bisphosphate	pH 7.5, 25°C, wild-type	Escherichia coli

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Release 2023.1 (January 2023)