Structural Basis of Phosphodiesterase 6 Inhibition by the C-terminal Region of the Gamma-subunit

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 2009 Oct 3

PMID 19798052

Citations 42

Authors

Brandy Barren

Lokesh Gakhar

Hakim Muradov

Kimberly K Boyd

S Ramaswamy

Nikolai O Artemyev

Affiliations

Soon will be listed here.

Abstract

The inhibitory interaction of phosphodiesterase-6 (PDE6) with its gamma-subunit (Pgamma) is pivotal in vertebrate phototransduction. Here, crystal structures of a chimaeric PDE5/PDE6 catalytic domain (PDE5/6cd) complexed with sildenafil or 3-isobutyl-1-methylxanthine and the Pgamma-inhibitory peptide Pgamma(70-87) have been determined at 2.9 and 3.0 A, respectively. These structures show the determinants and the mechanism of the PDE6 inhibition by Pgamma and suggest the conformational change of Pgamma on transducin activation. Two variable H- and M-loops of PDE5/6cd form a distinct interface that contributes to the Pgamma-binding site. This allows the Pgamma C-terminus to fit into the opening of the catalytic pocket, blocking cGMP access to the active site. Our analysis suggests that disruption of the H-M loop interface and Pgamma-binding site is a molecular cause of retinal degeneration in atrd3 mice. Comparison of the two PDE5/6cd structures shows an overlap between the sildenafil and Pgamma(70-87)-binding sites, thereby providing critical insights into the side effects of PDE5 inhibitors on vision.

Citing Articles

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References

. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994; 50(Pt 5):760-3. DOI: 10.1107/S0907444994003112. View

Artemyev N, Hamm H . Two-site high-affinity interaction between inhibitory and catalytic subunits of rod cyclic GMP phosphodiesterase. Biochem J. 1992; 283 ( Pt 1):273-9. PMC: 1131025. DOI: 10.1042/bj2830273. View

Artemyev N, Natochin M, Busman M, Schey K, Hamm H . Mechanism of photoreceptor cGMP phosphodiesterase inhibition by its gamma-subunits. Proc Natl Acad Sci U S A. 1996; 93(11):5407-12. PMC: 39259. DOI: 10.1073/pnas.93.11.5407. View

Murshudov G, Vagin A, Dodson E . Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr. 1997; 53(Pt 3):240-55. DOI: 10.1107/S0907444996012255. View

Mou H, Cote R . The catalytic and GAF domains of the rod cGMP phosphodiesterase (PDE6) heterodimer are regulated by distinct regions of its inhibitory gamma subunit. J Biol Chem. 2001; 276(29):27527-34. DOI: 10.1074/jbc.M103316200. View

Hart A, McKie L, Morgan J, Gautier P, West K, Jackson I . Genotype-phenotype correlation of mouse pde6b mutations. Invest Ophthalmol Vis Sci. 2005; 46(9):3443-50. DOI: 10.1167/iovs.05-0254. View

Granovsky A, Natochin M, Artemyev N . The gamma subunit of rod cGMP-phosphodiesterase blocks the enzyme catalytic site. J Biol Chem. 1997; 272(18):11686-9. DOI: 10.1074/jbc.272.18.11686. View

Granovsky A, Artemyev N . A conformational switch in the inhibitory gamma-subunit of PDE6 upon enzyme activation by transducin. Biochemistry. 2001; 40(44):13209-15. DOI: 10.1021/bi011127j. View

Stockman A, Sharpe L, Tufail A, Kell P, Jeffery G . Viagra slows the visual response to flicker. Curr Biol. 2006; 16(2):R44-5. DOI: 10.1016/j.cub.2006.01.016. View

10.

Guo L, Muradov H, Hajipour A, Sievert M, Artemyev N, Ruoho A . The inhibitory gamma subunit of the rod cGMP phosphodiesterase binds the catalytic subunits in an extended linear structure. J Biol Chem. 2006; 281(22):15412-22. DOI: 10.1074/jbc.M600595200. View

11.

Fu Y, Yau K . Phototransduction in mouse rods and cones. Pflugers Arch. 2007; 454(5):805-19. PMC: 2877390. DOI: 10.1007/s00424-006-0194-y. View

12.

Cote R . Characteristics of photoreceptor PDE (PDE6): similarities and differences to PDE5. Int J Impot Res. 2004; 16 Suppl 1:S28-33. DOI: 10.1038/sj.ijir.3901212. View

13.

Pflugrath J . The finer things in X-ray diffraction data collection. Acta Crystallogr D Biol Crystallogr. 1999; 55(Pt 10):1718-25. DOI: 10.1107/s090744499900935x. View

14.

Liu X, Bulgakov O, Wen X, Woodruff M, Pawlyk B, Yang J . AIPL1, the protein that is defective in Leber congenital amaurosis, is essential for the biosynthesis of retinal rod cGMP phosphodiesterase. Proc Natl Acad Sci U S A. 2004; 101(38):13903-8. PMC: 518851. DOI: 10.1073/pnas.0405160101. View

15.

Laties A, Sharlip I . Ocular safety in patients using sildenafil citrate therapy for erectile dysfunction. J Sex Med. 2006; 3(1):12-27. DOI: 10.1111/j.1743-6109.2005.00194.x. View

16.

Tsang S, Burns M, Calvert P, Gouras P, Baylor D, Goff S . Role for the target enzyme in deactivation of photoreceptor G protein in vivo. Science. 1998; 282(5386):117-21. DOI: 10.1126/science.282.5386.117. View

17.

Granovsky A, Artemyev N . Identification of the gamma subunit-interacting residues on photoreceptor cGMP phosphodiesterase, PDE6alpha '. J Biol Chem. 2000; 275(52):41258-62. DOI: 10.1074/jbc.M008094200. View

18.

Song J, Guo L, Muradov H, Artemyev N, Ruoho A, Markley J . Intrinsically disordered gamma-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure. Proc Natl Acad Sci U S A. 2008; 105(5):1505-10. PMC: 2234174. DOI: 10.1073/pnas.0709558105. View

19.

Slepak V, Artemyev N, Zhu Y, Dumke C, Sabacan L, Sondek J . An effector site that stimulates G-protein GTPase in photoreceptors. J Biol Chem. 1995; 270(24):14319-24. DOI: 10.1074/jbc.270.24.14319. View

20.

Takemoto D, Hurt D, Oppert B, Cunnick J . Domain mapping of the retinal cyclic GMP phosphodiesterase gamma-subunit. Function of the domains encoded by the three exons of the gamma-subunit gene. Biochem J. 1992; 281 ( Pt 3):637-43. PMC: 1130737. DOI: 10.1042/bj2810637. View