title: Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling.
abstract: Photoreceptor phosphodiesterase (PDE6) is the central effector enzyme in visual excitation pathway in rod and cone photoreceptors. Its tight regulation is essential for the speed, sensitivity, recovery and adaptation of visual detection. Although major steps in the PDE6 activation/deactivation pathway have been identified, mechanistic understanding of PDE6 regulation is limited by the lack of knowledge about the molecular organization of the PDE6 holoenzyme (αβγγ). Here, we characterize the PDE6 holoenzyme by integrative structural determination of the PDE6 catalytic dimer (αβ), based primarily on chemical cross-linking and mass spectrometric analysis. Our models built from high-density cross-linking data elucidate a parallel organization of the two catalytic subunits, with juxtaposed α-helical segments within the tandem regulatory GAF domains to provide multiple sites for dimerization. The two catalytic domains exist in an open configuration when compared to the structure of PDE2 in the apo state. Detailed structural elements for differential binding of the γ-subunit to the GAFa domains of the α- and β-subunits are revealed, providing insight into the regulation of the PDE6 activation/deactivation cycle.
authors.affiliation: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Zeng-Elmore
authors.affiliation: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA.
authors.forename: Xiong-Zhuo
authors.initials: XZ
authors.lastname: Gao
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Pellarin
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.
authors.forename: Dina
authors.initials: D
authors.lastname: Schneidman-Duhovny
authors.affiliation: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA.
authors.forename: Xiu-Jun
authors.initials: XJ
authors.lastname: Zhang
authors.affiliation: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA.
authors.forename: Katie A
authors.initials: KA
authors.lastname: Kozacka
authors.affiliation: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA.
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
authors.affiliation: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Chalkley
authors.affiliation: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA.
authors.forename: Rick H
authors.initials: RH
authors.lastname: Cote
authors.affiliation: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA. Electronic address: feixia.chu@unh.edu.
authors.forename: Feixia
authors.initials: F
authors.lastname: Chu
mesh_terms: D000818:Animals; D020134:Catalytic Domain; D002417:Cattle; D002853:Chromatography, Liquid; D003432:Cross-Linking Reagents / Q000494:pharmacology*; D054707:Cyclic Nucleotide Phosphodiesterases, Type 6 / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D005136:Eye Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D010446:Peptide Fragments / Q000032:analysis; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D012160:Retina / Q000187:drug effects / Q000201:enzymology*; D053719:Tandem Mass Spectrometry
chemical_list: D003432:Cross-Linking Reagents; D005136:Eye Proteins; D010446:Peptide Fragments; D054707:Cyclic Nucleotide Phosphodiesterases, Type 6
keywords: chemical cross-linking; integrative modeling; mass spectrometry; phosphodiesterase 6 (PDE6); visual transduction