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

Lead Research Organisation: University of St Andrews
Department Name: Chemistry


See proposal from Edinburgh,

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 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 In a genetic disease that leads to early death and progressive degeneration, there is a mutation in the enzyme couples Serine to palmitoyl Co-A. We have worked on the bacterial enzyme and now understand why the mutation perturbs the enzyme.
Exploitation Route It could be used to develop new treatments.
Sectors Healthcare

Description The finding were the first molecular insight into the degenerative disease, Hereditary Sensory and Autonomic Neuropathies.
First Year Of Impact 2009
Sector Healthcare
Impact Types Societal

Description Schools visits 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Each year I host visits to my lab from local secondary school (10's of pupils) and I also give a talk to visiting school pupils on science (approx 50 pupils).

Some of the children seemed to appreciate that chemistry was important in biology.
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,
Description Training and workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Between 20 to 50 pupils per year visit St Andrews and as part of this, they are exposed to structural biology.

Teachers report increased enthusiasm for biomedical science
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010
Description workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Helped in the training of post-graduate students in structural biology at the following meetings.
CCP4/ZCAM workshop, Zaragoza, Spain March 2012
CCP4/ APS workshop, Argonne, USA, June 2012
CCP4/APS workshop, Argonne, USA, June 2013
CCP4/CeBEM workshop, Montevideo, Uruguay, April 2013

Widespread use of UK authored software.
Year(s) Of Engagement Activity 2013,2014