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Literature summary extracted from

  • Chittori, S.; Simanshu, D.K.; Banerjee, S.; Murthy, A.M.; Mathivanan, S.; Savithri, H.S.; Murthy, M.R.
    Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies (2013), Biochim. Biophys. Acta, 1834, 2036-2044.
    View publication on PubMed

Activating Compound

EC Number Activating Compound Comment Organism Structure
2.7.2.15 acetate
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 ATP
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 Butyrate
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 CTP
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 dATP
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 dCTP
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 dGTP
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 GTP
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 propionate
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 TTP
-
Salmonella enterica subsp. enterica serovar Typhimurium

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.7.2.15 purified enzyme in complex with ATP, GTP, or CTP, soaking of crystals in 0.1 M Bis-Tris, pH 6.5, 35% pentaerythritol ethoxylate, crystals of enzyme StTdcD in complex with phosphate, AMP, ATP, Ap4, GMP, GDP, GTP, CMP and CTP are obtained using variations of crystallization conditions reported for the unliganded enzyme, X-ray diffraction structure determination and analyis at 2.4-3.0 A resolution, molecular replacement method using a polyalanine model of the unliganded StTdcD protomer, PDB ID 2E1Y as the search model, modeling Salmonella enterica subsp. enterica serovar Typhimurium

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.7.2.15 2-oxoglutarate feedback inhibition Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 citrate feedback inhibition Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 malate feedback inhibition Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 succinate feedback inhibition Salmonella enterica subsp. enterica serovar Typhimurium

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.7.2.15 additional information
-
additional information Michaelis-Menten kinetic analysis, the enzyme shows open and closed states consistent with inter-domain motion during catalysis Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 2 14 UTP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 2.5
-
propanoate pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 25.3
-
acetate pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 35.2
-
Butyrate pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 115
-
GTP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 126
-
ATP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 226
-
CTP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.2.15 Co2+ activates Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 Mg2+ activates, required. Free Mg2+ competes with the catalytically suitable ATP-Mg2+ complex for binding to the enzyme, consistent with the conformational differences observed in the binding of phosphate moiety of a nucleotide in the presence or absence of a metal ion Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 Mn2+ activates Salmonella enterica subsp. enterica serovar Typhimurium

Organism

EC Number Organism UniProt Comment Textmining
2.7.2.15 Salmonella enterica subsp. enterica serovar Typhimurium O06961 gene tdcD
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.2.15 ATP + acetate
-
Salmonella enterica subsp. enterica serovar Typhimurium ADP + acetyl phosphate
-
r
2.7.2.15 ATP + butyrate
-
Salmonella enterica subsp. enterica serovar Typhimurium ADP + butanoyl phosphate
-
r
2.7.2.15 ATP + propanoate
-
Salmonella enterica subsp. enterica serovar Typhimurium ADP + propanoyl phosphate
-
r
2.7.2.15 CTP + propanoate
-
Salmonella enterica subsp. enterica serovar Typhimurium CDP + propanoyl phosphate
-
r
2.7.2.15 GTP + propanoate
-
Salmonella enterica subsp. enterica serovar Typhimurium GDP + propanoyl phosphate
-
r
2.7.2.15 additional information enzyme binding of nucleotide mainly involves hydrophobic interactions with the base moiety and can account for the broad biochemical specificity observed between the enzyme and nucleotides, modeling. Residue Ala88 is an important residue involved in determining the rate of catalysis with short-chain fatty acid substrates. No activity with with several closely related analogues such as formate, isobutyrate, 2-oxobutyrate, malic acid, citrate, isocitric acid, oxaloacetate, succinate and 2-oxoglutarate, and also no activit with short-chain alcohols methanol, ethanol, propanol, and butanol, and aldehydes acetaldehyde and propionaldehyde. An ethylene glycol molecule bound sufficiently close to the gamma-phosphate in StTdcD complexes with triphosphate nucleotides supports direct in-line phosphoryl transfer Salmonella enterica subsp. enterica serovar Typhimurium ?
-
?
2.7.2.15 UTP + propanoate
-
Salmonella enterica subsp. enterica serovar Typhimurium UDP + propanoyl phosphate
-
r

Subunits

EC Number Subunits Comment Organism
2.7.2.15 More molecular dynamics simulations on monomeric and dimeric forms of enzyme StTdcD, modeling, overview Salmonella enterica subsp. enterica serovar Typhimurium

Synonyms

EC Number Synonyms Comment Organism
2.7.2.15 TdcD
-
Salmonella enterica subsp. enterica serovar Typhimurium

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.7.2.15 25
-
assay at Salmonella enterica subsp. enterica serovar Typhimurium

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.7.2.15 60
-
Butyrate pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 73
-
CTP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 81
-
UTP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 108
-
propanoate pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 113
-
GTP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 120
-
ATP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 120
-
acetate pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.7.2.15 7.5
-
assay at Salmonella enterica subsp. enterica serovar Typhimurium

Cofactor

EC Number Cofactor Comment Organism Structure
2.7.2.15 ATP
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 CTP
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 GTP
-
Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 additional information enzyme binding of nucleotide mainly involves hydrophobic interactions with the base moiety and can account for the broad biochemical specificity observed between the enzyme and nucleotides, modeling Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 UTP
-
Salmonella enterica subsp. enterica serovar Typhimurium

General Information

EC Number General Information Comment Organism
2.7.2.15 physiological function propionate kinase catalyzes reversible transfer of the gamma-phosphate of ATP to propionate during L-threonine degradation to propionate with broad ligand specificity Salmonella enterica subsp. enterica serovar Typhimurium

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
2.7.2.15 0.26
-
UTP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 0.31
-
CTP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 1
-
ATP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 1
-
GTP pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 1.7
-
Butyrate pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 4.7
-
acetate pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
2.7.2.15 43.2
-
propanoate pH 7.5, 25°C Salmonella enterica subsp. enterica serovar Typhimurium