Literature summary extracted from

Nurmohamed, S.; Vincent, H.A.; Titman, C.M.; Chandran, V.; Pears, M.R.; Du, D.; Griffin, J.L.; Callaghan, A.J.; Luisi, B.F.
Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli (2011), J. Biol. Chem., 286, 14315-14323.

Activating Compound

EC Number	Activating Compound	Comment	Organism	Structure
2.7.7.8	citrate	a PNPase-mediated response to citrate, and PNPase deletion broadly impacts on the metabolome. PNPase-dependent cells show reduced growth in the presence of increased citrate concentration. In vitro, citrate directly binds and modulates PNPase activity, and the enzyme is inhibited by binding of metal-chelated citrate, predominantly complexed as magnesium-citrate, in the active site at physiological concentrations. In the contrary, metal-free citrate is bound at a vestigial active site, where it stimulates PNPase activity, this vestigial site as an allosteric binding pocket that recognizes metal-free citrate	Escherichia coli

Cloned(Commentary)

EC Number	Cloned (Comment)	Organism
2.7.7.8	expression of enzyme mutant R153A/R372A/R405A/R409A in Escherichia coli strain BL21(DE3)	Escherichia coli

Protein Variants

EC Number	Protein Variants	Comment	Organism
2.7.7.8	additional information	construction of a strain in which PNPase activity is uncoupled from the degradosome through the deletion of the C-terminal degradosome-scaffold-ing domain of RNase E. Compared with the parental strain, significant differences are distributed across many metabolic pathways, including the Krebs cycle, amino acid synthesis, and glycolysis in the mutant strain. Salient differences are seen for amino acids and increases in the concentrations of succinate, fumarate, and malate, suggesting uncoupling of the two halves of the Krebs cycle	Escherichia coli
2.7.7.8	R153A/R372A/R405A/R409A	site-directed mutagenesis	Escherichia coli

Inhibitors

EC Number	Inhibitors	Comment	Organism	Structure
2.7.7.8	citrate	a PNPase-mediated response to citrate, and PNPase deletion broadly impacts on the metabolome. PNPase-dependent cells show reduced growth in the presence of increased citrate concentration. In vitro, citrate directly binds and modulates PNPase activity, and the enzyme is inhibited by binding of metal-chelated citrate, predominantly complexed as magnesium-citrate, in the active site at physiological concentrations. In the contrary, metal-free citrate is bound at a vestigial active site, where it stimulates PNPase activity	Escherichia coli

Metals/Ions

EC Number	Metals/Ions	Comment	Organism	Structure
2.7.7.8	Mg2+	required	Escherichia coli
2.7.7.8	Mn2+	manganese can substitute for magnesium as the catalytic metal in PNPase, and RNA degradation	Escherichia coli

Natural Substrates/ Products (Substrates)

EC Number	Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
2.7.7.8	RNAn+1 + phosphate	Escherichia coli	in addition to its degradative role, PNPase can also function as a polymerase, adding 3' tails to transcripts. The reverse of degradation is favored when nucleoside diphosphate rather than inorganic phosphate is present in excess	RNAn + a nucleoside diphosphate	-	r
2.7.7.8	RNAn+1 + phosphate	Escherichia coli MG1655	in addition to its degradative role, PNPase can also function as a polymerase, adding 3' tails to transcripts. The reverse of degradation is favored when nucleoside diphosphate rather than inorganic phosphate is present in excess	RNAn + a nucleoside diphosphate	-	r

Organism

EC Number	Organism	UniProt	Comment	Textmining
2.7.7.8	Escherichia coli	-	-	-
2.7.7.8	Escherichia coli MG1655	-	-	-

Substrates and Products (Substrate)

EC Number	Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
2.7.7.8	RNAn+1 + phosphate	in addition to its degradative role, PNPase can also function as a polymerase, adding 3' tails to transcripts. The reverse of degradation is favored when nucleoside diphosphate rather than inorganic phosphate is present in excess	Escherichia coli	RNAn + a nucleoside diphosphate	-	r
2.7.7.8	RNAn+1 + phosphate	substrates used for the forward degradation reaction are poly(rA) 15-mer RNA and phosphate	Escherichia coli	RNAn + a nucleoside diphosphate	substrates used for the reverse polymerization reaction are poly(rA) 15-mer RNA and ADP	r
2.7.7.8	RNAn+1 + phosphate	in addition to its degradative role, PNPase can also function as a polymerase, adding 3' tails to transcripts. The reverse of degradation is favored when nucleoside diphosphate rather than inorganic phosphate is present in excess	Escherichia coli MG1655	RNAn + a nucleoside diphosphate	-	r
2.7.7.8	RNAn+1 + phosphate	substrates used for the forward degradation reaction are poly(rA) 15-mer RNA and phosphate	Escherichia coli MG1655	RNAn + a nucleoside diphosphate	substrates used for the reverse polymerization reaction are poly(rA) 15-mer RNA and ADP	r

Synonyms

EC Number	Synonyms	Comment	Organism
2.7.7.8	PNPase	-	Escherichia coli
2.7.7.8	polynucleotide phosphorylase	-	Escherichia coli

Temperature Optimum [°C]

EC Number	Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
2.7.7.8	25	-	assay at	Escherichia coli

pH Optimum

EC Number	pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
2.7.7.8	7.5	-	assay at, reverse polymerization reaction	Escherichia coli
2.7.7.8	8	-	assay at, forward degradation reaction	Escherichia coli

General Information

EC Number	General Information	Comment	Organism
2.7.7.8	metabolism	the Krebs cycle metabolite citrate affects the activity of Escherichia coli polynucleotide phosphorylase (PNPase) and, conversely, that cellular metabolism is affected widely by PNPase activity, a PNPase-mediated response to citrate, and PNPase deletion broadly impacts on the metabolome and on global gene expression, detailed overview	Escherichia coli
2.7.7.8	physiological function	metabolite-bound PNPase structure and evidence for an allosteric pocket, overview	Escherichia coli

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Release 2023.1 (January 2023)