PDBsum entry 2e3p

Lipid transport

PDB id: 2e3p

Contents

Protein chain

235 a.a. *

Ligands

16C ×2

Waters ×391

* Residue conservation analysis

PDB id:

2e3p

Name:

Lipid transport

Title:

Crystal structure of cert start domain in complex with c16-cearmide (p1)

Structure:

Lipid-transfer protein cert. Chain: a, b. Fragment: cert start domain (residues 347-598). Synonym: goodpasture-antigen binding protein, gpbp, cdna flj34532 fis, clone hlung2008235, highly similar to homo sapiens goodpasture antigen-binding protein (col4a3bp)mRNA. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cert. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.40Å R-factor: 0.219 R-free: 0.251

Authors:

N.Kudo,K.Kumagai,S.Wakatsuki,M.Nishijima,K.Hanada,R.Kato

Key ref:

N.Kudo et al. (2008). Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide. Proc Natl Acad Sci U S A, 105, 488-493. PubMed id: 18184806 DOI: 10.1073/pnas.0709191105

Date:

28-Nov-06 Release date: 18-Dec-07

Protein chains

Q9Y5P4  (C43BP_HUMAN) -  Ceramide transfer protein from Homo sapiens

Seq: 624 a.a.

Struc: 235 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.0709191105

Proc Natl Acad Sci U S A 105:488-493 (2008)

PubMed id: 18184806

Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide.

N.Kudo, K.Kumagai, N.Tomishige, T.Yamaji, S.Wakatsuki, M.Nishijima, K.Hanada, R.Kato.

ABSTRACT

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.

Selected figure(s)

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.

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.

Figures were selected by an automated process.