5T4X image
Entry Detail
PDB ID:
5T4X
Title:
CRYSTAL STRUCTURE OF PDE6D IN APO-STATE
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2016-08-30
Release Date:
2018-01-10
Method Details:
Experimental Method:
Resolution:
1.81 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Chain IDs:A
Chain Length:170
Number of Molecules:1
Biological Source:Mus musculus
Primary Citation
Mechanistic insights into the role of prenyl-binding protein PrBP/ delta in membrane dissociation of phosphodiesterase 6.
Nat Commun 9 90 90 (2018)
PMID: 29311697 DOI: 10.1038/s41467-017-02569-y

Abstact

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.

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