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Literature summary for 2.3.1.50 extracted from

  • Raman, M.C.; Johnson, K.A.; Yard, B.A.; Lowther, J.; Carter, L.G.; Naismith, J.H.; Campopiano, D.J.
    The external aldimine form of serine palmitoyltransferase: structural, kinetic, and spectroscopic analysis of the wild-type enzyme and HSAN1 mutant mimics (2009), J. Biol. Chem., 284, 17328-17339.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 2.3.1.50

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) Sphingomonas paucimobilis

Crystallization (Commentary)

Crystallization (Comment) Organism
purified His-tagged recombinant wild-type and mutant enzymes in complex with cofactor and substrates, wild-type enzyme from 10 mM Tris, pH 7.5, 150 mM NaCl, and 0.025 mM or 0.250 mM pyridoxal 5'-phosphate, different conditions for the mutants, overview. Mass spectroscopic structure analysis, overview Sphingomonas paucimobilis

Protein Variants

Protein Variants Comment Organism
N100C site-directed mutagenesis, the mutation mimics the wild-type human enzyme and is fully active, crystal structure analysis Sphingomonas paucimobilis
N100W site-directed mutagenesis, the mutation mimics the mutation in the human enzyme causing hereditary sensory autonomic neuropathy type 1, the mutant shows reduced activity compared to the wild-type enzyme. The mutation affects the chemistry of the pyridoxal 5'-phosphate, crystal structure analysis Sphingomonas paucimobilis
N100Y site-directed mutagenesis, N100Y is less able to stabilize a quinonoid intermediate, the mutation mimics the mutation in the human enzyme causing hereditary sensory autonomic neuropathy type 1, the mutant shows reduced activity compared to the wild-type enzyme. The mutation affects the chemistry of the pyridoxal 5'-phosphate. The L-Ser external aldimine structure N100Y reveals significant differences that hinder the movement of a catalytically important Arg378 residue into the active site, crystal structure analysis Sphingomonas paucimobilis
R378A site-directed mutagenesis, crystal structure analysis, the mutant is less able to stabilize a quinonoid intermediate Sphingomonas paucimobilis
R378N site-directed mutagenesis, crystal structure analysis Sphingomonas paucimobilis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.019
-
 palmitoyl-CoA pH 7.5, 37°C, recombinant mutant N100W Sphingomonas paucimobilis
0.031
-
 palmitoyl-CoA pH 7.5, 37°C, recombinant mutant N100Y Sphingomonas paucimobilis
0.031
-
 palmitoyl-CoA pH 7.5, 37°C, recombinant mutant R378N Sphingomonas paucimobilis
0.035
-
 palmitoyl-CoA pH 7.5, 37°C, recombinant wild-type enzyme Sphingomonas paucimobilis
0.039
-
 palmitoyl-CoA pH 7.5, 37°C, recombinant mutant R378A Sphingomonas paucimobilis
0.06
-
 palmitoyl-CoA pH 7.5, 37°C, recombinant mutant N100C Sphingomonas paucimobilis
1.4
-
 L-serine pH 7.5, 37°C, recombinant wild-type enzyme Sphingomonas paucimobilis
1.6
-
 L-serine pH 7.5, 37°C, recombinant mutant N100W Sphingomonas paucimobilis
2.4
-
 L-serine pH 7.5, 37°C, recombinant mutant R378N Sphingomonas paucimobilis
2.5
-
 L-serine pH 7.5, 37°C, recombinant mutant N100Y Sphingomonas paucimobilis
3.8
-
 L-serine pH 7.5, 37°C, recombinant mutant R378A Sphingomonas paucimobilis
7
-
 L-serine pH 7.5, 37°C, recombinant mutant N100C Sphingomonas paucimobilis

Localization

Localization Comment Organism GeneOntology No. Textmining
membrane bound Homo sapiens 16020
-
membrane bound Sphingomonas paucimobilis 16020
-

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
palmitoyl-CoA + L-serine Homo sapiens
-
 CoA + 3-dehydro-D-sphinganine + CO2
-
 ?
palmitoyl-CoA + L-serine Sphingomonas paucimobilis
-
 CoA + 3-dehydro-D-sphinganine + CO2
-
 ?
palmitoyl-CoA + L-serine Sphingomonas paucimobilis EY2395
-
 CoA + 3-dehydro-D-sphinganine + CO2
-
 ?

Organism

Organism UniProt Comment Textmining
Homo sapiens
-
-
-
Sphingomonas paucimobilis Q93UV0
-
-
Sphingomonas paucimobilis EY2395 Q93UV0
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration Sphingomonas paucimobilis

Reaction

Reaction Comment Organism Reaction ID
palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2 the enzyme forms an external aldimine intermediate, as well as dunathan and quinoid intermediates, and followed by external beta-keto acid intermediate, and finally product quinoid and product external aldimine intermediates, reaction cycle, overview Sphingomonas paucimobilis
a
palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2 the enzyme forms an external aldimine intermediate, as well as dunathan and quinoid intermediates, followed by external beta-keto acid intermediate, and finally product quinoid and product external aldimine intermediates, reaction cycle, overview Homo sapiens
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
palmitoyl-CoA + L-serine
-
 Homo sapiens CoA + 3-dehydro-D-sphinganine + CO2
-
 ?
palmitoyl-CoA + L-serine
-
 Sphingomonas paucimobilis CoA + 3-dehydro-D-sphinganine + CO2
-
 ?
palmitoyl-CoA + L-serine
-
 Sphingomonas paucimobilis EY2395 CoA + 3-dehydro-D-sphinganine + CO2
-
 ?

Subunits

Subunits Comment Organism
heterodimer structure comparison with the SPT from Sphingomonas paucimobilis, overview Homo sapiens
homodimer structure comparison with the human SPT, overview Sphingomonas paucimobilis

Synonyms

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

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
 assay at Sphingomonas paucimobilis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.005
-
 L-serine recombinant mutant N100Y Sphingomonas paucimobilis
0.005
-
 palmitoyl-CoA recombinant mutant N100Y Sphingomonas paucimobilis
0.009
-
 L-serine recombinant mutant N100W Sphingomonas paucimobilis
0.009
-
 palmitoyl-CoA recombinant mutant N100W Sphingomonas paucimobilis
0.033
-
 L-serine recombinant mutant R378N Sphingomonas paucimobilis
0.033
-
 palmitoyl-CoA recombinant mutant R378N Sphingomonas paucimobilis
0.078
-
 L-serine recombinant mutant R378A Sphingomonas paucimobilis
0.078
-
 palmitoyl-CoA recombinant mutant R378A Sphingomonas paucimobilis
0.25
-
 L-serine recombinant mutant N100C Sphingomonas paucimobilis
0.25
-
 palmitoyl-CoA recombinant mutant N100C Sphingomonas paucimobilis
1.15
-
 L-serine recombinant wild-type enzyme Sphingomonas paucimobilis
1.15
-
 palmitoyl-CoA recombinant wild-type enzyme 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 Homo sapiens
pyridoxal 5'-phosphate dependent on, bound at the active site at the dimer interface Sphingomonas paucimobilis

General Information

General Information Comment Organism
malfunction mutations in human SPT cause hereditary sensory autonomic neuropathy type 1, HSAN1, a disease characterized by loss of feeling in extremities and severe pain Homo sapiens
metabolism SPT catalyzes the first and rate-limiting step of the sphingolipid biosynthetic pathway Homo sapiens

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.002
-
 L-serine pH 7.5, 37°C, recombinant mutant N100Y Sphingomonas paucimobilis
0.006
-
 L-serine pH 7.5, 37°C, recombinant mutant N100W Sphingomonas paucimobilis
0.014
-
 L-serine pH 7.5, 37°C, recombinant mutant R378N Sphingomonas paucimobilis
0.021
-
 L-serine pH 7.5, 37°C, recombinant mutant R378A Sphingomonas paucimobilis
0.036
-
 L-serine pH 7.5, 37°C, recombinant mutant N100C Sphingomonas paucimobilis
0.821
-
 L-serine pH 7.5, 37°C, recombinant wild-type enzyme Sphingomonas paucimobilis