PDBsum entry 4jgx

Lipid binding protein

PDB id: 4jgx

Contents

Protein chains

119 a.a.

128 a.a.

Ligands

CIT ×2

PLM ×2

Waters ×75

PDB id:

4jgx

Name:

Lipid binding protein

Title:

The structure of sterol carrier protein 2 from the yeast yarrowia lipolytica

Structure:

Fatty acid-binding protein. Chain: a, b. Synonym: sterol carrier protein 2, ylscp2. Engineered: yes

Source:

Yarrowia lipolytica. Yeast. Organism_taxid: 284591. Strain: cx-121-1b. Gene: scp2, yali0e01298g. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.188 R-free: 0.217

Authors:

F.P.De Berti,S.Capaldi,J.P.Acierno,S.Klinke,H.L.Monaco,M.R.Ermacora

Key ref:

F.P.De Berti et al. (2013). 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 Genomics, 14, 145-153. PubMed id: 24241823

Date:

04-Mar-13 Release date: 18-Dec-13

Protein chain

P80547  (SCP2_YARLI) -  Fatty acid-binding protein from Yarrowia lipolytica (strain CLIB 122 / E 150)

Seq: 129 a.a.

Struc: 119 a.a.

Protein chain

P80547  (SCP2_YARLI) -  Fatty acid-binding protein from Yarrowia lipolytica (strain CLIB 122 / E 150)

Seq: 129 a.a.

Struc: 128 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

J Struct Funct Genomics 14:145-153 (2013)

PubMed id: 24241823

The crystal structure of sterol carrier protein 2 from Yarrowia lipolytica and the evolutionary conservation of a large, non-specific lipid-binding cavity.

F.P.De Berti, S.Capaldi, R.Ferreyra, N.Burgardt, J.P.Acierno, S.Klinke, H.L.Monaco, M.R.Ermácora.

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.