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PDBsum entry 2jg2
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References listed in PDB file
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Key reference
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Title
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The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis.
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Authors
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B.A.Yard,
L.G.Carter,
K.A.Johnson,
I.M.Overton,
M.Dorward,
H.Liu,
S.A.Mcmahon,
M.Oke,
D.Puech,
G.J.Barton,
J.H.Naismith,
D.J.Campopiano.
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Ref.
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J Mol Biol, 2007,
370,
870-886.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 2.
Figure 2. Proposed reaction mechanism of SPT. (a)
Transaldimination of internal aldimine (holo-SPT), I with
L-serine to form external aldimine, II; (b) deprotonation of
C^α by base to form quinonoid, III; (c) Claisen condensation to
form putative β-ketoacid-aldimine complex, IV; (d)
decarboxylation to form product quinonoid, V; (e) reprotonation
of quinonoid to form product external aldimine, VI (f) release
of product 3-ketodihydrosphingosine (KDS) and regeneration of I.
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Figure 7.
Figure 7. Stereo view showing the proximity of the Asn100
residue of monomer B to the PLP cofactor of monomer A in the S.
paucimobilis SPT homodimer. Monomer A is drawn in green and
monomer B is drawn in blue. Asn100 of monomer B is shown in CPK.
Using the sequence alignment in Figure 9, the S. paucimobilis
SPT Asn100 residue maps to residue Cys133 on the SPT1 subunit of
human SPT. Mutations at this residue C133W and C133Y are known
to cause the autosomal disease hereditary sensory and autonomic
neuropathy type I (HSAN1). The conserved residues His159 and
His234 which interact directly with the PLP cofactor are also
highlighted.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
370,
870-886)
copyright 2007.
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