Abstract
Isoprenylated proteins are associated with membranes and their inter-compartmental distribution is regulated by solubilization factors, which incorporate lipid moieties in hydrophobic cavities and thereby facilitate free diffusion during trafficking. Here we report the crystal structure of a solubilization factor, the prenyl-binding protein (PrBP/δ), at 1.81 Å resolution in its ligand-free apo-form. Apo-PrBP/δ harbors a preshaped, deep hydrophobic cavity, capacitating apo-PrBP/δ to readily bind its prenylated cargo. To investigate the molecular mechanism of cargo solubilization we analyzed the PrBP/δ-induced membrane dissociation of rod photoreceptor phosphodiesterase (PDE6). The results suggest that PrBP/δ exclusively interacts with the soluble fraction of PDE6. Depletion of soluble species in turn leads to dissociation of membrane-bound PDE6, as both are in equilibrium. This “solubilization by depletion” mechanism of PrBP/δ differs from the extraction of prenylated proteins by the similar folded solubilization factor RhoGDI, which interacts with membrane bound cargo via an N-terminal structural element lacking in PrBP/δ.
Highlights
Isoprenylated proteins are associated with membranes and their inter-compartmental distribution is regulated by solubilization factors, which incorporate lipid moieties in hydrophobic cavities and thereby facilitate free diffusion during trafficking
We found in the cavity some, but not well-defined, electron density which indicate the presence of a flexible, small and polar molecule
We investigated the interaction of PrBP/δ with the rod photoreceptor cGMP phosphodiesterase 6 (PDE6)
Summary
Isoprenylated proteins are associated with membranes and their inter-compartmental distribution is regulated by solubilization factors, which incorporate lipid moieties in hydrophobic cavities and thereby facilitate free diffusion during trafficking. Depletion of soluble species in turn leads to dissociation of membrane-bound PDE6, as both are in equilibrium This “solubilization by depletion” mechanism of PrBP/δ differs from the extraction of prenylated proteins by the similar folded solubilization factor RhoGDI, which interacts with membrane bound cargo via an N-terminal structural element lacking in PrBP/δ. Several solubilization factors comprise similar 3D-structures despite low primary sequence homology[4,6,7] They were originally termed GDI or GDI-like (guaninenucleotide dissociation inhibitors) proteins, due to the discovery of RhoGDI (Ras-homolog GDI) and RabGDI (Ras-related in brain GDI) that interact with prenylated RhoGTPase and RabGTPase proteins, respectively[4,6]. In its simplest form, the PrBP/δ trafficking cycle comprises three steps: (i) solubilization of the prenylated protein (cargo) from its donor membrane by complex formation with PrBP/δ, (ii) targeting to the destination membrane by association of cargobound PrBP/δ with a peripherally membrane bound docking protein (e.g., RPGR; Retinitis Pigmentosa GTPase Regulator) that acts as a receptor for PrBP/δ, and (iii) dissociation of the ternary PrBP/δ–cargo–RPGR–complex by interaction of PrBP/δ with displacement factors (e.g., Arl-2-GTP; Arf-like protein) which allows release of the cargo into the destination membrane, as well as recycling of PrBP/δ
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