Serine palmitoyltransferase / structure and function of the first enzyme in sphingolipid biosynthesis.

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Chemistry


All cell walls have to be tough and durable and provide a physical barrier to protect the cell from external factors. They have to keep the cell contents inside but also allow molecules (e.g. nutrients) to pass into the cell and waste to leave. Humans, plants and bacteria have different cell wall components and they are made up of numerous complex building blocks called sphingolipids. It was recently discovered that the chemical reaction at the start of the sphingolipid synthetic pathway in all species is the same and begins by connecting an amino acid to a fatty acid. This reaction is catalysed by an enzyme called serine palmitoyltransferase (SPT) and is dependent on a B vitamin cofactor. We'd like to understand in molecular detail how sphingolipid membranes are made. Studying sphingolipid chemistry and the enzymes that make them in humans and plants is difficult because the building blocks and enzymes are embedded in membranes. To make it easier to study them, it helps to extract them into water and to do this we have to use detergents. Unfortunately, the enzymes often stop working in water. However, a bacterium (called Sphingomonas) was discovered that makes only one type of sphingolipid and its SPT enzyme is soluble in water. We can purify milligram amounts of this SPT and we have recently determined its 3D molecular structure to atomic resolution. We'd now like to understand how it catalyses the chemical reaction and how it can be inhibited. It turns out that sphingolipids not only play structural roles in cells, but also regulate and control the way the cell works. Inhibitors of sphingolipid production might turn out to be new anti-cancer or anti-inflammatory drugs. We can use our bacterial water-soluble SPT structure as a model for the human membrane-bound enzyme. Also, it has been discovered that some people have a neurological disease where their SPT enzyme is mutated so we can also use our model to understand how these mutations can cause problems with spingolipid chemistry in the brain.

Technical Summary

Sphingolipid biosynthesis commences with the condensation of L-serine and palmitoyl-CoA to produce 3-ketodihydrosphingosine (KDS). This reaction is catalysed by the PLP-dependent enzyme serine palmitoyltransferase (SPT) which is a member of a larger family of enzyme catalysing Claisen condensation reactions. SPT is a membrane-bound heterodimer (SPT1/SPT2) in eukaryotes such as humans and yeast and a cytoplasmic homodimer in the Gram-negative bacterium Sphingomonas paucimobilis. Unusually, the outer membrane of S. paucimobilis contains glycosphingolipid (GSL) instead of lipopolysaccharide (LPS), and SPT catalyses the first step of the GSL biosynthetic pathway in this organism. We have determined the crystal structure of the holo-form of S. paucimobilis SPT at 1.3 Å resolution. The enzyme is a symmetrical homodimer with two active sites and a monomeric tertiary structure consisting of three domains. The PLP cofactor is bound covalently to a lysine residue (Lys265) as an internal aldimine/Schiff base and the active site is composed of residues from both subunits, located at the bottom of a deep cleft. We have generated models of the human SPT1/SPT2 heterodimer from the bacterial structure by bioinformatic analysis. Mutations in the human SPT1-encoding subunit have been shown to cause a neuropathological disease known as hereditary sensory and autonomic neuropathy type I (HSAN1). In the proposed study, we will build from this platform to explore the substrate specificity and catalytic mechanism of this enzyme with a range of substrates, products and inhibitors using a combination of spectroscopy, crystallography, chemical analysis and informatics. We will use the bacterial SPT as a model to study mutations in SPT1 that cause HSAN1 disorders and make SPT fusions to investigate recently discovered viral fused SPTs.
Description We studied the mechanism of this important enzyme, SPT. We understood how the bacterial enzyme catalysed its reaction and also used this as a model for the analysis of mutants found in the human enzyme.
Exploitation Route We can use the SPT structure to design specific inhibitors that may of use in mammalian studies.
Sectors Pharmaceuticals and Medical Biotechnology

Description We were contacted by a USA family (Deater) in 2008 that are affected by a rare genetic condition - a neuropathic disease - HSN1. This is caused by mutations in the SPT enzyme. The PI was invited to Boston to discuss the results of his research on SPT in the context of finding a treatment for HSN1
First Year Of Impact 2008
Sector Pharmaceuticals and Medical Biotechnology
Impact Types Societal

Description SPT purification 
Organisation Manchester University NHS Foundation Trust
Department Biochemistry
Country United Kingdom 
Sector Hospitals 
PI Contribution Purify human SPT during post-doc visit
Collaborator Contribution Provide clones and purification methods
Impact another BBSRC grant was funded
Start Year 2010