2JG2

HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE

Summary for 2JG2

• Entry DOI: 10.2210/pdb2jg2/pdb
• Related: 2JGT
• Descriptor: SERINE PALMITOYLTRANSFERASE, PYRIDOXAL-5'-PHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: spt, plp, sspf, transferase, sphingolipid, pyridoxal phosphate, serine palmitoyl transferase
• Biological source: PSEUDOMONAS PAUCIMOBILIS
• Total number of polymer chains: 1
• Total formula weight: 45604.33

Authors

Yard, B.A.,Carter, L.G.,Johnson, K.A.,Overton, I.M.,Mcmahon, S.A.,Dorward, M.,Liu, H.,Puech, D.,Oke, M.,Barton, G.J.,Naismith, J.H.,Campopiano, D.J. (deposition date: 2007-02-07, release date: 2007-05-01, Last modification date: 2015-11-11)

Primary citation

Yard, B.A.,Carter, L.G.,Johnson, K.A.,Overton, I.M.,Dorward, M.,Liu, H.,Mcmahon, S.A.,Oke, M.,Puech, D.,Barton, G.J.,Naismith, J.H.,Campopiano, D.J.
The Structure of Serine Palmitoyltransferase; Gateway to Sphingolipid Biosynthesis.
J.Mol.Biol., 370:870-, 2007

PubMed Abstract: 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; EC 2.3.1.50), which 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 report here the crystal structure of the holo-form of S. paucimobilis SPT at 1.3 A 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. Models of the human SPT1/SPT2 heterodimer were generated from the bacterial structure by bioinformatics 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). Our models provide an understanding of how these mutations may affect the activity of the enzyme.

PubMed: 17559874
DOI: 10.1016/J.JMB.2007.04.086

Experimental method

X-RAY DIFFRACTION (1.3 Å)