6OVP

Sterol Carrier Protein 2 from Yarrowia Lipolytica (apo form)

Summary for 6OVP

• Entry DOI: 10.2210/pdb6ovp/pdb
• Related: 4JGX
• Descriptor: Fatty acid-binding protein, PHOSPHATE ION (3 entities in total)
• Functional Keywords: lipid binding protein, non specific lipid transfer, long chain fatty acids and coa esters
• Biological source: Yarrowia lipolytica
• Total number of polymer chains: 2
• Total formula weight: 28205.13

Authors

Gianotti, A.R.,Klinke, S.,Ermacora, M.R. (deposition date: 2019-05-08, release date: 2020-05-20, Last modification date: 2023-10-11)

Primary citation

Gianotti, A.R.,Klinke, S.,Ermacora, M.R.
The structure of unliganded sterol carrier protein 2 from Yarrowia lipolytica unveils a mechanism for binding site occlusion.
J.Struct.Biol., 213:107675-107675, 2020

PubMed Abstract: Isolated or as a part of multidomain proteins, Sterol Carrier Protein 2 (SCP2) exhibits high affinity and broad specificity for different lipidic and hydrophobic compounds. A wealth of structural information on SCP2 domains in all forms of life is currently available; however, many aspects of its ligand binding activity are poorly understood. ylSCP2 is a well-characterized single domain SCP2 from the yeast Yarrowia lipolytica. Herein, we report the X-ray structure of unliganded ylSCP2 refined to 2.0 Å resolution. Comparison with the previously solved liganded ylSCP2 structure unveiled a novel mechanism for binding site occlusion. The liganded ylSCP2 binding site is a large cavity with a volume of more than 800 Å. In unliganded ylSCP2 the binding site is reduced to about 140 Å. The obliteration is caused by a swing movement of the C-terminal α helix 5 and a subtle compaction of helices 2-4. Previous pairwise comparisons were between homologous SCP2 domains with a uncertain binding status. The reported unliganded ylSCP2 structure allows for the first time a fully controlled comparative analysis of the conformational effects of ligand occupation dispelling several doubts regarding the architecture of SCP2 binding site.

PubMed: 33278583
DOI: 10.1016/j.jsb.2020.107675

Experimental method

X-RAY DIFFRACTION (1.991 Å)