Literature summary for 2.7.2.15 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.

Activating Compound

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

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

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

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
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	14	UTP	pH 7.5, 25°C	Salmonella enterica subsp. enterica serovar Typhimurium
2.5	-	propanoate	pH 7.5, 25°C	Salmonella enterica subsp. enterica serovar Typhimurium
25.3	-	acetate	pH 7.5, 25°C	Salmonella enterica subsp. enterica serovar Typhimurium
35.2	-	Butyrate	pH 7.5, 25°C	Salmonella enterica subsp. enterica serovar Typhimurium
115	-	GTP	pH 7.5, 25°C	Salmonella enterica subsp. enterica serovar Typhimurium
126	-	ATP	pH 7.5, 25°C	Salmonella enterica subsp. enterica serovar Typhimurium
226	-	CTP	pH 7.5, 25°C	Salmonella enterica subsp. enterica serovar Typhimurium

Metals/Ions

Metals/Ions	Comment	Organism
Co2+	activates	Salmonella enterica subsp. enterica serovar Typhimurium
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
Mn2+	activates	Salmonella enterica subsp. enterica serovar Typhimurium

Organism

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

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
ATP + acetate	-	Salmonella enterica subsp. enterica serovar Typhimurium	ADP + acetyl phosphate	-	r
ATP + butyrate	-	Salmonella enterica subsp. enterica serovar Typhimurium	ADP + butanoyl phosphate	-	r
ATP + propanoate	-	Salmonella enterica subsp. enterica serovar Typhimurium	ADP + propanoyl phosphate	-	r
CTP + propanoate	-	Salmonella enterica subsp. enterica serovar Typhimurium	CDP + propanoyl phosphate	-	r
GTP + propanoate	-	Salmonella enterica subsp. enterica serovar Typhimurium	GDP + propanoyl phosphate	-	r
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	?	-	?
UTP + propanoate	-	Salmonella enterica subsp. enterica serovar Typhimurium	UDP + propanoyl phosphate	-	r

Subunits

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

Synonyms

Synonyms	Comment	Organism
TdcD	-	Salmonella enterica subsp. enterica serovar Typhimurium

Temperature Optimum [°C]

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

Turnover Number [1/s]

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

pH Optimum

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

Cofactor

Cofactor	Comment	Organism
ATP	-	Salmonella enterica subsp. enterica serovar Typhimurium
CTP	-	Salmonella enterica subsp. enterica serovar Typhimurium
GTP	-	Salmonella enterica subsp. enterica serovar Typhimurium
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
UTP	-	Salmonella enterica subsp. enterica serovar Typhimurium

General Information

General Information	Comment	Organism
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]

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