PXD020817

PXD020817 is an original dataset announced via ProteomeXchange.

Title	Structural analysis of the regulatory GAF domains of cGMP phosphodiesterase elucidates the allosteric communication pathway
Description	Regulation of photoreceptor phosphodiesterase (PDE6) activity is responsible for the speed, sensitivity, and recovery of the photoresponse during visual signaling in vertebrate photoreceptor cells. It is hypothesized that the physiological differences in the light responsiveness of rods and cones may result in part from differences in the structure and regulation of the distinct isoforms of rod and cone PDE6. Although rod and cone PDE6 catalytic subunits share a similar domain organization consisting of tandem GAF domains (GAFa and GAFb) and a catalytic domain, cone PDE6 is a homodimer whereas rod PDE6 consists of two homologous catalytic subunits. Here we provide the x-ray crystal structure of cone GAFab regulatory domain solved at 3.3 Å resolution, in conjunction with chemical cross-linking and mass spectrometric analysis of conformational changes to GAFab induced upon binding of cGMP and the PDE6 inhibitory γ-subunit (Pγ). Ligand-induced changes in cross-linked residues implicate multiple conformational changes in the GAFa and GAFb domains in forming an allosteric communication network that communicates with the PDE6 catalytic domains. Molecular dynamics (MD) simulations of cone GAFab revealed asymmetry in the two GAFab subunits forming the homodimer and allosteric perturbations on cGMP binding. Cross-linking of Pγ to GAFab in conjunction with solution NMR spectroscopy of isotopically labeled Pγ identified the central polycationic region of Pγ interacting with the GAFb domain. These results provide a mechanistic basis for developing allosteric activators of PDE6 with therapeutic implications for halting the progression of several retinal degenerative diseases.
HostingRepository	PRIDE
AnnounceDate	2022-02-15
AnnouncementXML	Submission_2022-02-15_13:01:51.818.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Richa Gupta
SpeciesList	scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive HF; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-10 00:16:02	ID requested
⏵ 1	2022-02-15 13:01:52	announced

Gupta R, Liu Y, Wang H, Nordyke CT, Puterbaugh RZ, Cui W, Varga K, Chu F, Ke H, Vashisth H, Cote RH, Structural Analysis of the Regulatory GAF Domains of cGMP Phosphodiesterase Elucidates the Allosteric Communication Pathway. J Mol Biol, 432(21):5765-5783(2020) [pubmed]

submitter keyword: PDE6, allosteric regulation, structural biology, x-ray crystallography, nuclear magnetic resonance spectroscopy, chemical cross-linking, mass spectrometry, integrative structural modeling,

Rick Cote
contact affiliation	Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, NH, USA
contact email	Rick.Cote@unh.edu
lab head
Richa Gupta
contact affiliation	University of New Hampshire
contact email	Richa.gupta@unh.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD020817
     1. Label: PRIDE project
     2. Name: Structural analysis of the regulatory GAF domains of cGMP phosphodiesterase elucidates the allosteric communication pathway