Literature summary for 2.3.1.50 extracted from

Beattie, A.E.; Clarke, D.J.; Wadsworth, J.M.; Lowther, J.; Sin, H.L.; Campopiano, D.J.
Reconstitution of the pyridoxal 5-phosphate (PLP) dependent enzyme serine palmitoyltransferase (SPT) with pyridoxal reveals a crucial role for the phosphate during catalysis (2013), Chem. Commun. (Camb. ), 49, 7058-7060.

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KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	Michaelis-Menten kinetics.The regenerated enzyme displays similar Km and kcat values to the purified enzyme, with only a small increase in the Km for L-serine	Sphingomonas paucimobilis
0.0356	-	palmitoyl-CoA	recombinant wild-type enzyme, pH 7.5, 25°C	Sphingomonas paucimobilis
1.6	-	L-serine	recombinant wild-type enzyme, pH 7.5, 25°C	Sphingomonas paucimobilis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
palmitoyl-CoA + L-serine	Sphingomonas paucimobilis	-	CoA + 3-dehydro-D-sphinganine + CO2	-	?

Organism

Organism	UniProt	Comment	Textmining
Sphingomonas paucimobilis	Q93UV0	-	-

Reaction

Reaction	Comment	Organism	Reaction ID
palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2	the reaction proceeds via several intermediate states, the pyridoxal 5'-phosphate cofactor binds to an active site lysine residue as an internal aldimine/Schiffs base (I). The L-serine displaces the lysine residue (Lys265) to form the PLP-L-serine external aldimine (II). Deprotonation of II gives a carbanion/quinonoid species (III) which condenses in a Claisen-like manner with the acyl-CoA thioester substrate to form a PLP-beta-keto acid, which then decarboxylates to generate the PLP-KDS product quinonoid (IV). This then reprotonates to form PLP-KDS aldimine (V) which is finally displaced by Lys265. The step releasing CoA and CO2 and producing the quinonoid intermediate species is irreversible. Interaction between the hydroxyl group of the L-serine substrate and the 5'-phosphate group of pyridoxal 5'-phosphate occurs in the formation of the external aldimine II, overview	Sphingomonas paucimobilis	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
additional information	no activity with L-phosphoserine	Sphingomonas paucimobilis	?	-	?
palmitoyl-CoA + L-serine	-	Sphingomonas paucimobilis	CoA + 3-dehydro-D-sphinganine + CO2	-	?
palmitoyl-CoA + L-serine	interaction between the hydroxyl group of the L-serine substrate and the 5'-phosphate group of pyridoxal 5'-phosphate. This interaction is important for substrate specificity and optimal catalytic efficiency	Sphingomonas paucimobilis	CoA + 3-dehydro-D-sphinganine + CO2	-	?

Synonyms

Synonyms	Comment	Organism
serine palmitoyltransferase	-	Sphingomonas paucimobilis
SPT	-	Sphingomonas paucimobilis

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
25	-	assay at	Sphingomonas paucimobilis

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
1.54	-	L-serine	recombinant wild-type enzyme, pH 7.5, 25°C	Sphingomonas paucimobilis

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Sphingomonas paucimobilis

Cofactor

Cofactor	Comment	Organism	Structure
pyridoxal 5'-phosphate	dependent on, bound by lysine 265 residue, interaction between the hydroxyl group of the L-serine substrate and the 5'-phosphate group of pyridoxal 5'-phosphate. This interaction is important for substrate specificity and optimal catalytic efficiency	Sphingomonas paucimobilis

General Information

General Information	Comment	Organism
evolution	the enzyme belongs to the PLP-superfamily and a member of the alpha-oxoamine synthase family (AOS, fold type I)	Sphingomonas paucimobilis
additional information	the interaction between the hydroxyl group of the L-serine substrate and the 5'-phosphate group of pyridoxal 5'-phosphate is important for substrate specificity and optimal catalytic efficiency. Structure of the PLP-L-serine external aldimine intermediate of the enzyme, PDB ID 2W8J, overview	Sphingomonas paucimobilis
physiological function	the enzyme is required for de novo sphingolipid biosynthesis	Sphingomonas paucimobilis

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
0.9625	-	L-serine	recombinant wild-type enzyme, pH 7.5, 25°C	Sphingomonas paucimobilis

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Release 2023.1 (January 2023)