5T4X

CRYSTAL STRUCTURE OF PDE6D IN APO-STATE

Summary for 5T4X

• Entry DOI: 10.2210/pdb5t4x/pdb
• Descriptor: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (2 entities in total)
• Functional Keywords: immunoglobulin-like beta sandwitch, pde6 delta, farnesyl, lipid binding protein, prenyl binding protein, geranylgeranyl, transport protein, phosphodiesterase 6, rhodopsin, membrane dissociation, apo-state, membrane trafficking, cellular trafficking, rhodopsin kinase, ras-gtpase
• Biological source: Mus musculus (Mouse)
• Cellular location: Cytoplasm, cytosol : O55057
• Total number of polymer chains: 1
• Total formula weight: 19540.31

Authors

Qureshi, B.M.,Schmidt, A.,Scheerer, P. (deposition date: 2016-08-30, release date: 2018-01-10, Last modification date: 2024-01-17)

Primary citation

Qureshi, B.M.,Schmidt, A.,Behrmann, E.,Burger, J.,Mielke, T.,Spahn, C.M.T.,Heck, M.,Scheerer, P.
Mechanistic insights into the role of prenyl-binding protein PrBP/ delta in membrane dissociation of phosphodiesterase 6.
Nat Commun, 9:90-90, 2018

PubMed 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.

PubMed: 29311697
DOI: 10.1038/s41467-017-02569-y

Experimental method

X-RAY DIFFRACTION (1.81 Å)