The Structure of Serine Palmitoyltransferase; Gateway to Sphingolipid Biosynthesis

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 su...

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Published inJournal of molecular biology Vol. 370; no. 5; pp. 870 - 886
Main Authors Yard, Beverley A., Carter, Lester G., Johnson, Kenneth A., Overton, Ian M., Dorward, Mark, Liu, Huanting, McMahon, Stephen A., Oke, Muse, Puech, Daphné, Barton, Geoffrey J., Naismith, James H., Campopiano, Dominic J.
Format Journal Article
LanguageEnglish
Published England Elsevier Ltd 27.07.2007
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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 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. 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.
AbstractList 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.
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 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. 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.
Author Yard, Beverley A.
Campopiano, Dominic J.
McMahon, Stephen A.
Puech, Daphné
Liu, Huanting
Oke, Muse
Overton, Ian M.
Dorward, Mark
Barton, Geoffrey J.
Carter, Lester G.
Naismith, James H.
Johnson, Kenneth A.
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  givenname: James H.
  surname: Naismith
  fullname: Naismith, James H.
  organization: Centre for Biomolecular Sciences, Scottish Structural Proteomics Facility, The University of St. Andrews, Fife KY16 9ST, Scotland, UK
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  surname: Campopiano
  fullname: Campopiano, Dominic J.
  email: Dominic.Campopiano@ed.ac.uk
  organization: School of Chemistry, EaStCHEM, The University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, Scotland, UK
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Keywords hereditary sensory and autonomic neuropathy type I
GSL
ALAS
HSAN1
AOS
sphingolipids
LCB
RMSD
serine palmitoyltransferase
AONS
LPS
X-ray crystallography
CoA
KBL
PLP
SPT
bioinformatics
KDS
Language English
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Snippet Sphingolipid biosynthesis commences with the condensation of L-serine and palmitoyl-CoA to produce 3-ketodihydrosphingosine (KDS). This reaction is catalysed...
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SubjectTerms Amino Acid Sequence
Bacterial Proteins - chemistry
Bacterial Proteins - physiology
Binding Sites
bioinformatics
Computational Biology
Dimerization
hereditary sensory and autonomic neuropathy type I
Holoenzymes - chemistry
Humans
Models, Molecular
Molecular Sequence Data
Mutation
Protein Conformation
Protein Subunits - chemistry
Protein Subunits - genetics
Protein Subunits - physiology
Serine C-Palmitoyltransferase - chemistry
Serine C-Palmitoyltransferase - genetics
Serine C-Palmitoyltransferase - physiology
serine palmitoyltransferase
sphingolipids
Sphingolipids - biosynthesis
Sphingomonas - enzymology
Sphingomonas paucimobilis
X-ray crystallography
Title The Structure of Serine Palmitoyltransferase; Gateway to Sphingolipid Biosynthesis
URI https://dx.doi.org/10.1016/j.jmb.2007.04.086
https://www.ncbi.nlm.nih.gov/pubmed/17559874
https://search.proquest.com/docview/19796088
https://search.proquest.com/docview/70627998
Volume 370
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