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PDBsum entry 2e3p
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Lipid transport
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PDB id
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2e3p
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References listed in PDB file
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Key reference
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Title
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Structural basis for specific lipid recognition by cert responsible for nonvesicular trafficking of ceramide.
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Authors
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N.Kudo,
K.Kumagai,
N.Tomishige,
T.Yamaji,
S.Wakatsuki,
M.Nishijima,
K.Hanada,
R.Kato.
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Ref.
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Proc Natl Acad Sci U S A, 2008,
105,
488-493.
[DOI no: ]
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PubMed id
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Abstract
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In mammalian cells, ceramide is synthesized in the endoplasmic reticulum and
transferred to the Golgi apparatus for conversion to sphingomyelin. Ceramide
transport occurs in a nonvesicular manner and is mediated by CERT, a cytosolic
68-kDa protein with a C-terminal steroidogenic acute regulatory protein-related
lipid transfer (START) domain. The CERT START domain efficiently transfers
natural D-erythro-C16-ceramide, but not lipids with longer (C20) amide-acyl
chains. The molecular mechanisms of ceramide specificity, both stereo-specific
recognition and length limit, are not well understood. Here we report the
crystal structures of the CERT START domain in its apo-form and in complex with
ceramides having different acyl chain lengths. In these complex structures, one
ceramide molecule is buried in a long amphiphilic cavity. At the far end of the
cavity, the amide and hydroxyl groups of ceramide form a hydrogen bond network
with specific amino acid residues that play key roles in stereo-specific
ceramide recognition. At the head of the ceramide molecule, there is no extra
space to accommodate additional bulky groups. The two aliphatic chains of
ceramide are surrounded by the hydrophobic wall of the cavity, whose size and
shape dictate the length limit for cognate ceramides. Furthermore, local
high-crystallographic B-factors suggest that the alpha-3 and the Omega1 loop
might work as a gate to incorporate the ceramide into the cavity. Thus, the
structures demonstrate the structural basis for the mechanism by which CERT can
distinguish ceramide from other lipid types yet still recognize multiple species
of ceramides.
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Figure 3.
Molecular surface of the CERT START domain in complex with
C[6]- (A), C[16]- (B), and C[18]- (C) ceramide cut at the level
of the cavity, respectively. Ceramide molecules are drawn as
sticks, in which yellow, blue, and red represent C, N, and O
atoms, respectively. Hydrophobic and polar/charged amino acid
residues inside the cavity are shown in green and blue,
respectively. The outer surface and the cross-section of the
CERT START domain are drawn in gray and in dark brown,
respectively.
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Figure 4.
Hydrogen bond network between the CERT START domain and
C[16]-ceramide (A). Large white letters, amino acid residues
interacting with the ceramide; small white letters, α-helix and
β-sheet strands, numbered; green meshes, ceramide omit map
contoured at 2.5 σ; orange dashed lines, hydrogen bonds; red
circles, water molecules. In the wire model, N and O atoms are
highlighted by blue and red, respectively. The ceramide molecule
(yellow) and the side chains of the CERT START domain are shown
by wire models. (B) Water-mediated stabilization of O1 oxygen of
ceramide viewed in the direction opposite to A.
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