PDBsum entry 5t4x

Transport protein

PDB id: 5t4x

Contents

Protein chain

148 a.a.

Waters ×90

PDB id:

5t4x

Name:

Transport protein

Title:

Crystal structure of pde6d in apo-state

Structure:

Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta. Chain: a. Synonym: gmp-pde delta. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: pde6d. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

1.81Å R-factor: 0.184 R-free: 0.214

Authors:

B.M.Qureshi,A.Schmidt,P.Scheerer

Key ref:

B.M.Qureshi et al. (2018). Mechanistic insights into the role of prenyl-binding protein PrBP/δ in membrane dissociation of phosphodiesterase 6. Nat Commun, 9, 90. PubMed id: 29311697

Date:

30-Aug-16 Release date: 10-Jan-18

Protein chain

O55057  (PDE6D_MOUSE) -  Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta from Mus musculus

Seq: 150 a.a.

Struc: 148 a.a.

Enzyme reactions

• Enzyme class: E.C.?

Nat Commun 9:90 (2018)

PubMed id: 29311697

Mechanistic insights into the role of prenyl-binding protein PrBP/δ in membrane dissociation of phosphodiesterase 6.

B.M.Qureshi, A.Schmidt, E.Behrmann, J.Bürger, T.Mielke, C.M.T.Spahn, M.Heck, P.Scheerer.

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.