4JGX

The Structure of Sterol Carrier Protein 2 from the Yeast Yarrowia Lipolytica

Summary for 4JGX

• Entry DOI: 10.2210/pdb4jgx/pdb
• Descriptor: Fatty acid-binding protein, CITRIC ACID, PALMITIC ACID, ... (4 entities in total)
• Functional Keywords: lipid binding protein, non specific lipid transfer, long chain fatty acids and coa esters
• Biological source: Yarrowia lipolytica (Yeast)
• Cellular location: Peroxisome (Potential): P80547
• Total number of polymer chains: 2
• Total formula weight: 29007.25

Authors

De Berti, F.P.,Capaldi, S.,Acierno, J.P.,Klinke, S.,Monaco, H.L.,Ermacora, M.R. (deposition date: 2013-03-04, release date: 2013-12-18, Last modification date: 2023-11-08)

Primary citation

De Berti, F.P.,Capaldi, S.,Ferreyra, R.,Burgardt, N.,Acierno, J.P.,Klinke, S.,Monaco, H.L.,Ermacora, M.R.
The crystal structure of sterol carrier protein 2 from Yarrowia lipolytica and the evolutionary conservation of a large, non-specific lipid-binding cavity.
J.Struct.Funct.Genom., 14:145-153, 2013

PubMed Abstract: Sterol carrier protein 2 (SCP2), a small intracellular domain present in all forms of life, binds with high affinity a broad spectrum of lipids. Due to its involvement in the metabolism of long-chain fatty acids and cholesterol uptake, it has been the focus of intense research in mammals and insects; much less characterized are SCP2 from other eukaryotic cells and microorganisms. We report here the X-ray structure of Yarrowia lipolytica SCP2 (YLSCP2) at 2.2 Å resolution in complex with palmitic acid. This is the first fungal SCP2 structure solved, and it consists of the canonical five-stranded β-sheet covered on the internal face by a layer of five α-helices. The overall fold is conserved among the SCP2 family, however, YLSCP2 is most similar to the SCP2 domain of human MFE-2, a bifunctional enzyme acting on peroxisomal β-oxidation. We have identified the common structural elements defining the shape and volume of the large binding cavity in all species characterized. Moreover, we found that the cavity of the SCP2 domains is distinctly formed by carbon atoms, containing neither organized water nor rigid polar interactions with the ligand. These features are in contrast with those of fatty acid binding proteins, whose internal cavities are more polar and contain bound water. The results will help to design experiments to unveil the SCP2 function in very different cellular contexts and metabolic conditions.

PubMed: 24241823
DOI: 10.1007/s10969-013-9166-6

Experimental method

X-RAY DIFFRACTION (2.2 Å)