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Literature summary for 2.3.1.50 extracted from

  • Ikushiro, H.; Islam, M.M.; Okamoto, A.; Hoseki, J.; Murakawa, T.; Fujii, S.; Miyahara, I.; Hayashi, H.
    Structural insights into the enzymatic mechanism of serine palmitoyltransferase from Sphingobacterium multivorum (2009), J. Biochem., 146, 549-562.
    View publication on PubMed

Activating Compound

Activating Compound Comment Organism Structure
S-(2-oxoheptadecyl)-CoA binds to the smSPT-external aldimine complex and enhances the exchange rate of the alpha-proton of L-serine by smSPT Sphingobacterium multivorum

Cloned(Commentary)

Cloned (Comment) Organism
SPT expression in Escherichia coli strain BL21(DE3) Sphingobacterium multivorum

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant enzyme complexed with L-serine, sitting drop vapor diffusion method, 0.002 ml of protein solution containing 20 mg/ml SPT, 20 mM potasium phosphate, pH 7.7, and 10 mM pyridoxal 5'-phosphate, is mixed with 0.004 ml of reservoir solution containing 100 mM Tris-HCl; pH 8.5, 200 mM sodium acetate, 21.6% w/v PEG 4000, equilibration against 0.5 ml reservoir solution at 20°C, 2 weeks, Schiff base formation between L-serine and pyridoxal 5'-phosphate in the crystal, X-ray diffraction structure determination and analysis at 2.3 A resolution, structural modelling Sphingobacterium multivorum

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
palmitoyl-CoA + L-serine Sphingobacterium multivorum
-
CoA + 3-dehydro-D-sphinganine + CO2
-
?
palmitoyl-CoA + L-serine Sphingobacterium multivorum GTC97
-
CoA + 3-dehydro-D-sphinganine + CO2
-
?

Organism

Organism UniProt Comment Textmining
Sphingobacterium multivorum A7BFV6
-
-
Sphingobacterium multivorum GTC97 A7BFV6
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant SPT from Escherichia coli strain BL21(DE3) Sphingobacterium multivorum

Reaction

Reaction Comment Organism Reaction ID
palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO2 via reaction intermediate pyridoxal 5'-phosphate-L-serine aldimine, His138 changes its hydrogen bond partner from the carboxyl group of L-serine to the carbonyl group of palmitoyl-CoA upon the binding of palmitoyl-CoA, making the L-serine Ca–H bond perpendicular to the pyridoxal 5'-phosphate-Schiff base plane, reaction mechanism with substrate synergism in the SPT reaction, overview. Modelling of reaction intermediates Sphingobacterium multivorum

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
palmitoyl-CoA + L-serine
-
Sphingobacterium multivorum CoA + 3-dehydro-D-sphinganine + CO2
-
?
palmitoyl-CoA + L-serine
-
Sphingobacterium multivorum GTC97 CoA + 3-dehydro-D-sphinganine + CO2
-
?

Synonyms

Synonyms Comment Organism
serine palmitoyltransferase
-
Sphingobacterium multivorum
SPT
-
Sphingobacterium multivorum

Cofactor

Cofactor Comment Organism Structure
pyridoxal 5'-phosphate
-
Sphingobacterium multivorum

General Information

General Information Comment Organism
metabolism SPT is a key enzyme of sphingolipid biosynthesis and catalyses the pyridoxal 5'-phosphate-dependent decarboxylative condensation reaction of L-serine with palmitoyl-CoA to generate 3-ketodihydrosphingosine Sphingobacterium multivorum