Literature summary for 3.6.1.40 extracted from

Song, H.; Dharmasena, M.N.; Wang, C.; Shaw, G.X.; Cherry, S.; Tropea, J.E.; Jin, D.J.; Ji, X.
Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori (2019), FEBS J., 287, 1865-1885 .

Cloned(Commentary)

Cloned (Comment)	Organism
expressed in Escherichia coli MG1655 cells	Helicobacter pylori
expressed in Escherichia coli MG1655 cells	Escherichia coli

Crystallization (Commentary)

Crystallization (Comment)	Organism
sitting drop vapor diffusion method, apoenzyme, using 10% (w/v) PEG 3350, 0.1 M HEPES (pH 7.5), and 0.2 M magnesium chloride	Escherichia coli
sitting drop vapor diffusion method. Apoenzyme, using 20% (w/v) PEG 3350, 0.2 M ammonium sulfate, and 15 mM malic acid. Enzyme in complex with 5'-guanosine-diphosphate-monothiophosphate or phosphoaminophosphonic acid guanylate ester, using 20% (w/v) PEG 3350 and 0.2 M potassium chloride. Enzyme in complex with guanosine tetraphosphate, using 20% (w/v) PEG 3350, 0.2 M ammonium tartrate, and 15 mM malic acid	Helicobacter pylori

Crystallization (Comment)

Organism

sitting drop vapor diffusion method, apoenzyme, using 10% (w/v) PEG 3350, 0.1 M HEPES (pH 7.5), and 0.2 M magnesium chloride

Escherichia coli

sitting drop vapor diffusion method. Apoenzyme, using 20% (w/v) PEG 3350, 0.2 M ammonium sulfate, and 15 mM malic acid. Enzyme in complex with 5'-guanosine-diphosphate-monothiophosphate or phosphoaminophosphonic acid guanylate ester, using 20% (w/v) PEG 3350 and 0.2 M potassium chloride. Enzyme in complex with guanosine tetraphosphate, using 20% (w/v) PEG 3350, 0.2 M ammonium tartrate, and 15 mM malic acid

Helicobacter pylori

Protein Variants

Protein Variants	Comment	Organism
D136A	the mutant shows severely reduced activity compared to the wild type enzyme	Helicobacter pylori
D9A	the mutant shows severely reduced activity compared to the wild type enzyme	Helicobacter pylori
E115A	the mutant shows severely reduced activity compared to the wild type enzyme	Helicobacter pylori
E143A	the mutant shows severely reduced activity compared to the wild type enzyme	Helicobacter pylori

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.02443	-	guanosine 5'-triphosphate 3'-diphosphate	at pH 7.4 and 37°C	Helicobacter pylori
0.04951	-	guanosine 5'-triphosphate 3'-diphosphate	at pH 7.4 and 37°C	Escherichia coli

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required for activity	Helicobacter pylori
Mg2+	required for activity	Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
guanosine 5'-triphosphate 3'-diphosphate + H2O	Helicobacter pylori	-	guanosine 3',5'-bis(diphosphate) + phosphate	-	?
guanosine 5'-triphosphate 3'-diphosphate + H2O	Escherichia coli	-	guanosine 3',5'-bis(diphosphate) + phosphate	-	?
guanosine 5'-triphosphate 3'-diphosphate + H2O	Helicobacter pylori B38	-	guanosine 3',5'-bis(diphosphate) + phosphate	-	?

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	P25552	-	-
Helicobacter pylori	C7BYL8	-	-
Helicobacter pylori B38	C7BYL8	-	-

Purification (Commentary)

Purification (Comment)	Organism
HisTrap column chromatography and Sephacryl S-200 gel filtration	Helicobacter pylori
HisTrap column chromatography and Sephacryl S-200 gel filtration	Escherichia coli

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
guanosine 5'-triphosphate 3'-diphosphate + H2O	-	Helicobacter pylori	guanosine 3',5'-bis(diphosphate) + phosphate	-	?
guanosine 5'-triphosphate 3'-diphosphate + H2O	-	Escherichia coli	guanosine 3',5'-bis(diphosphate) + phosphate	-	?
guanosine 5'-triphosphate 3'-diphosphate + H2O	-	Helicobacter pylori B38	guanosine 3',5'-bis(diphosphate) + phosphate	-	?

Subunits

Subunits	Comment	Organism
homodimer	2 * 113000, small-angle X-ray scattering	Helicobacter pylori
homotetramer	2 * 233000, small-angle X-ray scattering	Escherichia coli

Synonyms

Synonyms	Comment	Organism
GppA	-	Helicobacter pylori
GppA	-	Escherichia coli
pppGpp phosphohydrolase	-	Helicobacter pylori
pppGpp phosphohydrolase	-	Escherichia coli

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.044	-	guanosine 5'-triphosphate 3'-diphosphate	at pH 7.4 and 37°C	Helicobacter pylori
14.406	-	guanosine 5'-triphosphate 3'-diphosphate	at pH 7.4 and 37°C	Escherichia coli