Literature summary for 2.7.4.1 extracted from

Parnell, A.E.; Mordhorst, S.; Kemper, F.; Giurrandino, M.; Prince, J.P.; Schwarzer, N.J.; Hofer, A.; Wohlwend, D.; Jessen, H.J.; Gerhardt, S.; Einsle, O.; Oyston, P.C.F.; Andexer, J.N.; Roach, P.L.
Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures (2018), Proc. Natl. Acad. Sci. USA, 115, 3350-3355 .

Application

Application	Comment	Organism
biotechnology	polyphosphate kinases use inexpensive and stable polyphosphate as a phosphate donor and phosphorylate nucleoside 5'-monophosphate as well as 5'-diphosphates. This makes them of special interest for application in ATP regeneration systems, which can be efficiently coupled to ATP-consuming enzymes in environmentally friendly and sustainable biotechnological processes	Francisella tularensis subsp. tularensis
biotechnology	polyphosphate kinases use inexpensive and stable polyphosphate as a phosphate donor and phosphorylate nucleoside 5'-monophosphate as well as 5'-diphosphates. This makes them of special interest for application in ATP regeneration systems, which can be efficiently coupled to ATP-consuming enzymes in environmentally friendly and sustainable biotechnological processes	Meiothermus ruber

Crystallization (Commentary)

Crystallization (Comment)	Organism
structure to 1.9 A resolution, as the archetypal class III PPK2. PPK2 forms a crystallographic tetramer, each protomer consists of a five-stranded parallel beta-sheet surrounded by 10 alpha-helices. Comparison with the structure of Francisella tularensis PKK2, a class I PKK2	Meiothermus ruber
structure to 2.23 A resolution, class I PPK2. Comparison with the structure of Meiothermus ruber PKK2, a class III PKK2	Francisella tularensis subsp. tularensis
vapor diffusion method, enzyme complexed with polyphosphate and/or nucleotide substrate	Francisella tularensis subsp. tularensis
vapor diffusion method, enzyme complexed with polyphosphate and/or nucleotide substrate	Meiothermus ruber

Protein Variants

Protein Variants	Comment	Organism
D117N	about 300fold decrease in activity	Francisella tularensis subsp. tularensis
D117N	catalytic efficiency (kcat/Km) is 5.7fold higher than wild-type value	Francisella tularensis subsp. tularensis
D192A	about 10000fold decrease in activity	Francisella tularensis subsp. tularensis
D192A	catalytic efficiency (kcat/Km) is 12319fold lower than wild-type value	Francisella tularensis subsp. tularensis
D62A	about 1000fold decrease in activity	Francisella tularensis subsp. tularensis
D62A	catalytic efficiency (kcat/Km) is 900fold lower than wild-type value	Francisella tularensis subsp. tularensis
K66A	about 10000fold decrease in activity	Francisella tularensis subsp. tularensis
K66A	catalytic efficiency (kcat/Km) is 131590fold lower than wild-type value	Francisella tularensis subsp. tularensis
N121D	7fold decrease in activity with AMP, 25fold decrease in activity with ADP	Meiothermus ruber
N121D	the catalytic efficiency for ADP is 6.45fold lower than the wild-type value. The catalytic efficiency for AMP is 24fold lower than the wild-type value	Meiothermus ruber
R118A	about 10000fold decrease in activity	Francisella tularensis subsp. tularensis
R118A	catalytic efficiency (kcat/Km) is 15649fold lower than wild-type value	Francisella tularensis subsp. tularensis
R178A	about 10000fold decrease in activity	Francisella tularensis subsp. tularensis
R178A	catalytic efficiency (kcat/Km) is 6095fold lower than wild-type value	Francisella tularensis subsp. tularensis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.033	-	AMP	wild-type, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
0.033	-	ADP	wild-type enzyme, pH and temperature not specified in the publication	Meiothermus ruber
0.075	-	ADP	mutant enzyme N121D, pH and temperature not specified in the publication	Meiothermus ruber
0.075	-	AMP	mutant N121D, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
0.246	-	ADP	wild-type, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
0.246	-	AMP	wild-type enzyme, pH and temperature not specified in the publication	Meiothermus ruber
0.358	-	AMP	mutant enzyme N121D, pH and temperature not specified in the publication	Meiothermus ruber
0.358	-	ADP	mutant N121D, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
0.546	-	ADP	wild-type, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
2.47	-	ADP	mutant D62A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
2.47	-	ADP	mutant enzyme D62A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
3.21	-	ADP	mutant D192A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
3.21	-	ADP	mutant enzyme D192A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
3.25	-	ADP	mutant enzyme R178A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
3.25	-	ADP	mutant R178A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
4.03	-	ADP	mutant D117N, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
4.03	-	ADP	mutant enzyme D117N, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
6.18	-	ADP	mutant enzyme R118A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
6.18	-	ADP	mutant R118A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
9.546	-	ADP	wild-type enzyme, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
12.3	-	ADP	mutant enzyme K66A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
12.3	-	ADP	mutant K66A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
ADP + (phosphate)n+1	Francisella tularensis subsp. tularensis	-	ATP + (phosphate)n	-	?
ADP + (phosphate)n+1	Meiothermus ruber	-	ATP + (phosphate)n	-	?
ADP + (phosphate)n+1	Francisella tularensis subsp. tularensis Schu 4	-	ATP + (phosphate)n	-	?
ADP + (phosphate)n+1	Meiothermus ruber H328	-	ATP + (phosphate)n	-	?

Organism

Organism	UniProt	Comment	Textmining
Francisella tularensis subsp. tularensis	Q5NEQ5	-	-
Francisella tularensis subsp. tularensis	Q5NEQ5	cf. EC 2.7.4.34	-
Francisella tularensis subsp. tularensis Schu 4	Q5NEQ5	cf. EC 2.7.4.34	-
Meiothermus ruber	A0A806DL21	-	-
Meiothermus ruber	M9XB82	-	-
Meiothermus ruber	M9XB82	cf. EC 2.7.4.34	-
Meiothermus ruber DSM 1279	M9XB82	-	-
Meiothermus ruber H328	A0A806DL21	-	-
Meiothermus ruber NBRC 106122	M9XB82	cf. EC 2.7.4.34	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
ADP + (phosphate)n+1	-	Francisella tularensis subsp. tularensis	ATP + (phosphate)n	-	?
ADP + (phosphate)n+1	-	Francisella tularensis subsp. tularensis	ATP + (phosphate)n	-	r
ADP + (phosphate)n+1	-	Meiothermus ruber	ATP + (phosphate)n	-	?
ADP + (phosphate)n+1	-	Meiothermus ruber	ATP + (phosphate)n	-	r
ADP + (phosphate)n+1	-	Meiothermus ruber NBRC 106122	ATP + (phosphate)n	-	r
ADP + (phosphate)n+1	-	Francisella tularensis subsp. tularensis Schu 4	ATP + (phosphate)n	-	?
ADP + (phosphate)n+1	-	Francisella tularensis subsp. tularensis Schu 4	ATP + (phosphate)n	-	r
ADP + (phosphate)n+1	-	Meiothermus ruber H328	ATP + (phosphate)n	-	?
ADP + (phosphate)n+1	-	Meiothermus ruber DSM 1279	ATP + (phosphate)n	-	r
AMP + (phosphate)n+1	-	Meiothermus ruber	?	-	?
AMP + (phosphate)n+1	-	Meiothermus ruber H328	?	-	?
AMP + (phosphate)n+2	-	Francisella tularensis subsp. tularensis	ATP + (phosphate)n	-	r
AMP + (phosphate)n+2	-	Meiothermus ruber	ATP + (phosphate)n	-	r
AMP + (phosphate)n+2	-	Meiothermus ruber NBRC 106122	ATP + (phosphate)n	-	r
AMP + (phosphate)n+2	-	Francisella tularensis subsp. tularensis Schu 4	ATP + (phosphate)n	-	r
AMP + (phosphate)n+2	-	Meiothermus ruber DSM 1279	ATP + (phosphate)n	-	r

Subunits

Subunits	Comment	Organism
monomer	behaves as a monomer in the absence of substrate, but addition of polyphosphate promotes dimerization	Francisella tularensis subsp. tularensis
tetramer	tetrameric in the crystalline state	Francisella tularensis subsp. tularensis
tetramer	tetrameric in the crystalline state. Trimeric in solution the absence of substrates, but forms tetramers in the presence of polyphosphate	Meiothermus ruber
trimer	trimeric in solution the absence of substrates, but forms tetramers in the presence of polyphosphate	Meiothermus ruber

Synonyms

Synonyms	Comment	Organism
class I PPK2	-	Francisella tularensis subsp. tularensis
class III PPK2	-	Meiothermus ruber
K649_10090	-	Meiothermus ruber
Mrub_2488	-	Meiothermus ruber
polyphosphate kinase 2	class I polyphosphate kinase 2 preferentially phosphorylates nucleoside diphosphates	Francisella tularensis subsp. tularensis
polyphosphate kinase 2	class III polyphosphate kinase 2 can phosphorylate either nucleoside mono- or diphosphates	Meiothermus ruber

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
0.0015	-	ADP	mutant D192A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.0022	-	ADP	mutant R118A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.0031	-	ADP	mutant R178A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.0053	-	ADP	mutant K66A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.015	-	ADP	mutant N121D, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
0.016	-	ADP	mutant D62A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.032	-	ADP	wild-type, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.072	-	ADP	mutant D117N, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.15	-	ADP	mutant enzyme D192A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.22	-	ADP	mutant enzyme R118A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.246	-	ADP	wild-type, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
0.31	-	ADP	mutant enzyme R178A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.53	-	ADP	mutant enzyme K66A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
1.59	-	ADP	mutant enzyme D62A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
2.49	-	AMP	mutant N121D, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
7.1	-	AMP	wild-type, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
7.24	-	ADP	mutant enzyme D117N, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
317	-	ADP	wild-type enzyme, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis

General Information

General Information	Comment	Organism
drug target	polyphosphate kinases are involved in many metabolic processes in bacteria, including pathogenic species. As these enzymes are not present in animals, they are a prime target for the development of antibiotics	Francisella tularensis subsp. tularensis
drug target	polyphosphate kinases are involved in many metabolic processes in bacteria, including pathogenic species. As these enzymes are not present in animals, they are a prime target for the development of antibiotics	Meiothermus ruber

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
0.00037	-	ADP	mutant enzyme R118A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.00037	-	ADP	mutant R118A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.00044	-	ADP	mutant enzyme K66A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.00044	-	ADP	mutant K66A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.00047	-	ADP	mutant D192A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.00047	-	ADP	mutant enzyme D192A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.00095	-	ADP	mutant enzyme R178A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.00095	-	ADP	mutant R178A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.0064	-	ADP	mutant D62A, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.00643	-	ADP	mutant enzyme D62A, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
0.018	-	ADP	mutant D117N, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
4.1	-	ADP	mutant N121D, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
4.106	-	AMP	mutant enzyme N121D, pH and temperature not specified in the publication	Meiothermus ruber
5.79	-	ADP	wild-type, pH not specified in the publication, temperature not specified in the publication	Francisella tularensis subsp. tularensis
5.79	-	ADP	wild-type enzyme, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
33.2	-	ADP	mutant enzyme D117N, pH and temperature not specified in the publication	Francisella tularensis subsp. tularensis
33.2	-	ADP	mutant enzyme N121D, pH and temperature not specified in the publication	Meiothermus ruber
33.2	-	AMP	mutant N121D, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
100	-	ADP	wild-type, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
100	-	AMP	wild-type enzyme, pH and temperature not specified in the publication	Meiothermus ruber
214.2	-	AMP	wild-type, pH not specified in the publication, temperature not specified in the publication	Meiothermus ruber
214.2	-	ADP	wild-type enzyme, pH and temperature not specified in the publication	Meiothermus ruber