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Literature summary for 2.7.4.1 extracted from

  • Achbergerova, L.; Nahalka, J.
    Degradation of polyphosphates by polyphosphate kinases from Ruegeria pomeroyi (2014), Biotechnol. Lett., 36, 2029-2035.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
gene SPO0224, DNA and amino acid sequence determination and analysis, recombinant expression of Strep-tagged isozyme PPK2-3 in Escherichia coli strain BL21(DE3)-T1 Ruegeria pomeroyi
gene SPO1256, DNA and amino acid sequence determination and analysis, recombinant expression of STrep-tagged isoyzme PPK2-2 in Escherichia coli strain BL21(DE3)-T1 Ruegeria pomeroyi
gene SPO1727, DNA and amino acid sequence determination and analysis, recombinant expression of Strep-tagged isozyme PPK2-1 in Escherichia coli strain BL21(DE3)-T1 Ruegeria pomeroyi

Inhibitors

Inhibitors Comment Organism Structure
Co2+ complete inhibition; complete inhibition; complete inhibition Ruegeria pomeroyi
EDTA low inhibition; low inhibition Ruegeria pomeroyi

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.2
-
GDP pH 8.0, 30°C, recombinant isozyme PPK2-1 Ruegeria pomeroyi
2.5
-
ADP pH 8.0, 30°C, recombinant isozyme PPK2-2 Ruegeria pomeroyi
3.6
-
UDP pH 8.0, 30°C, recombinant isozyme PPK2-3 Ruegeria pomeroyi

Metals/Ions

Metals/Ions Comment Organism Structure
Ca2+ activates Ruegeria pomeroyi
Ca2+ activates, best cation Ruegeria pomeroyi
Mg2+ activates Ruegeria pomeroyi
Mg2+ activates, best cation Ruegeria pomeroyi
Mn2+ activates Ruegeria pomeroyi
Mn2+ activates, best cation Ruegeria pomeroyi
additional information enzyme SPO1727 requires a divalent cation, but shows no specificity, only Co2+ is not accepted, overview Ruegeria pomeroyi
additional information isozyme SPO0224 requires a divalent cation, but shows no specificity, only Co2+ is not accepted, overview Ruegeria pomeroyi
additional information isozyme SPO125 requires a divalent cation, but shows no specificity, only Co2+ is not accepted, overview Ruegeria pomeroyi
Ni2+ activates Ruegeria pomeroyi
Zn2+ activates Ruegeria pomeroyi

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
34750
-
calculated from sequence, SDS-PAGE Ruegeria pomeroyi
36720
-
calculated from sequence, SDS-PAGE Ruegeria pomeroyi
39950
-
calculated from sequence, SDS-PAGE Ruegeria pomeroyi

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ADP + (phosphate)n Ruegeria pomeroyi
-
ATP + (phosphate)n-1
-
?
ADP + (phosphate)n Ruegeria pomeroyi ATCC 700808
-
ATP + (phosphate)n-1
-
?
CDP + (phosphate)n Ruegeria pomeroyi
-
CTP + (phosphate)n-1
-
?
CDP + (phosphate)n Ruegeria pomeroyi ATCC 700808
-
CTP + (phosphate)n-1
-
?
GDP + (phosphate)n Ruegeria pomeroyi
-
GTP + (phosphate)n-1
-
?
GDP + (phosphate)n Ruegeria pomeroyi ATCC 700808
-
GTP + (phosphate)n-1
-
?
UDP + (phosphate)n Ruegeria pomeroyi
-
UTP + (phosphate)n-1
-
?
UDP + (phosphate)n Ruegeria pomeroyi ATCC 700808
-
UTP + (phosphate)n-1
-
?

Organism

Organism UniProt Comment Textmining
Ruegeria pomeroyi Q5LSN8 gene SPO1727, isozyme PPK2-1
-
Ruegeria pomeroyi Q5LU04 gene SPO1256, isozyme PPK2-2
-
Ruegeria pomeroyi Q5LX16 gene SPO0224, isozyme PPK2-3
-
Ruegeria pomeroyi ATCC 700808 Q5LSN8 gene SPO1727, isozyme PPK2-1
-
Ruegeria pomeroyi ATCC 700808 Q5LU04 gene SPO1256, isozyme PPK2-2
-
Ruegeria pomeroyi ATCC 700808 Q5LX16 gene SPO0224, isozyme PPK2-3
-

Purification (Commentary)

Purification (Comment) Organism
recombinant Strep-tagged isozyme PPK2-1 from Escherichia coli strain BL21(DE3) by streptavidin affinity chromatography Ruegeria pomeroyi
recombinant Strep-tagged isozyme PPK2-2 from Escherichia coli strain BL21(DE3) by streptavidin affinity chromatography Ruegeria pomeroyi
recombinant Strep-tagged isozyme PPK2-3 from Escherichia coli strain BL21(DE3) by streptavidin affinity chromatography Ruegeria pomeroyi

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ADP + (phosphate)n
-
Ruegeria pomeroyi ATP + (phosphate)n-1
-
?
ADP + (phosphate)n
-
Ruegeria pomeroyi ATCC 700808 ATP + (phosphate)n-1
-
?
CDP + (phosphate)n
-
Ruegeria pomeroyi CTP + (phosphate)n-1
-
?
CDP + (phosphate)n
-
Ruegeria pomeroyi ATCC 700808 CTP + (phosphate)n-1
-
?
GDP + (phosphate)n
-
Ruegeria pomeroyi GTP + (phosphate)n-1
-
?
GDP + (phosphate)n
-
Ruegeria pomeroyi ATCC 700808 GTP + (phosphate)n-1
-
?
additional information all PPK isozymes from Ruegeria pomeroyi accept all NDPs similarly and exhibit low NDP selectivity Ruegeria pomeroyi ?
-
?
additional information all PPK isozymes from Ruegeria pomeroyi accept all NDPs similarly and exhibit low NDP selectivity Ruegeria pomeroyi ATCC 700808 ?
-
?
UDP + (phosphate)n
-
Ruegeria pomeroyi UTP + (phosphate)n-1
-
?
UDP + (phosphate)n
-
Ruegeria pomeroyi ATCC 700808 UTP + (phosphate)n-1
-
?

Subunits

Subunits Comment Organism
monomer 1 * 34750, recombinant PPK2-3, sequence calculation and SDS-PAGE Ruegeria pomeroyi
monomer 1 * 36720, recombinant PPK2-1, sequence calculation and SDS-PAGE Ruegeria pomeroyi
monomer 1 * 39950, recombinant PPK2-2, sequence calculation and SDS-PAGE Ruegeria pomeroyi

Synonyms

Synonyms Comment Organism
polyphosphate kinase 2
-
Ruegeria pomeroyi
PPK2
-
Ruegeria pomeroyi
PPK2-1
-
Ruegeria pomeroyi
PPK2-2
-
Ruegeria pomeroyi
PPK2-3
-
Ruegeria pomeroyi
SPO0224
-
Ruegeria pomeroyi
SPO1256
-
Ruegeria pomeroyi
SPO1727
-
Ruegeria pomeroyi

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
assay at Ruegeria pomeroyi

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.18
-
GDP pH 8.0, 30°C, recombinant isozyme PPK2-1 Ruegeria pomeroyi
4.9
-
UDP pH 8.0, 30°C, recombinant isozyme PPK2-3 Ruegeria pomeroyi
5.22
-
ADP pH 8.0, 30°C, recombinant isozyme PPK2-2 Ruegeria pomeroyi

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
-
Ruegeria pomeroyi
8
-
optimum 1 Ruegeria pomeroyi
9
-
-
Ruegeria pomeroyi
10
-
optimum 2 Ruegeria pomeroyi

pH Range

pH Minimum pH Maximum Comment Organism
5 11 activity range, profile overview Ruegeria pomeroyi

General Information

General Information Comment Organism
evolution in general, all PPKs are ancient enzymes, and phylogenetic analysis indicates that the polyphosphate degradation process is older than polyphosphate synthesis. Additionally, PPK2 proteins are older than PPK1 enzymes Ruegeria pomeroyi

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.37
-
UDP pH 8.0, 30°C, recombinant isozyme PPK2-3 Ruegeria pomeroyi
2.08
-
ADP pH 8.0, 30°C, recombinant isozyme PPK2-2 Ruegeria pomeroyi
3.48
-
GDP pH 8.0, 30°C, recombinant isozyme PPK2-1 Ruegeria pomeroyi