Structural insights into the enzymatic mechanism of serine palmitoyltransferase from Sphingobacterium multivorum

J Biochem. 2009 Oct;146(4):549-62. doi: 10.1093/jb/mvp100. Epub 2009 Jun 29.


Serine palmitoyltransferase (SPT) is a key enzyme of sphingolipid biosynthesis and catalyses the pyridoxal 5'-phosphate (PLP)-dependent decarboxylative condensation reaction of l-serine with palmitoyl-CoA to generate 3-ketodihydrosphingosine. The crystal structure of SPT from Sphingobacterium multivorum GTC97 complexed with l-serine was determined at 2.3 A resolution. The electron density map showed the Schiff base formation between l-serine and PLP in the crystal. Because of the hydrogen bond formation with His138, the orientation of the Calpha-H bond of the PLP-l-serine aldimine was not perpendicular to the PLP-Schiff base plane. This conformation is unfavourable for the alpha-proton abstraction by Lys244 and the reaction is expected to stop at the PLP-l-serine aldimine. Structural modelling of the following intermediates indicated that 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 Calpha-H bond perpendicular to the PLP-Schiff base plane. These crystal and model structures well explained the observations on bacterial SPTs that the alpha-deprotonation of l-serine occurs only in the presence of palmitoyl-CoA. This study provides the structural evidence that directly supports our proposed mechanism of the substrate synergism in the SPT reaction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalysis
  • Crystallography, X-Ray
  • Models, Molecular
  • Palmitoyl Coenzyme A / chemistry
  • Palmitoyl Coenzyme A / metabolism
  • Protein Conformation
  • Protein Structure, Tertiary
  • Serine / chemistry
  • Serine C-Palmitoyltransferase / chemistry*
  • Serine C-Palmitoyltransferase / metabolism
  • Sphingobacterium / enzymology*
  • Sphingobacterium / metabolism
  • Sphingosine / analogs & derivatives
  • Sphingosine / chemical synthesis
  • Sphingosine / chemistry


  • ketodihydrosphingosine
  • Palmitoyl Coenzyme A
  • Serine
  • Serine C-Palmitoyltransferase
  • Sphingosine