Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling

J Mol Biol. 2014 Nov 11;426(22):3713-3728. doi: 10.1016/j.jmb.2014.07.033. Epub 2014 Aug 19.


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.

Keywords: chemical cross-linking; integrative modeling; mass spectrometry; phosphodiesterase 6 (PDE6); visual transduction.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Catalytic Domain
  • Cattle
  • Chromatography, Liquid
  • Cross-Linking Reagents / pharmacology*
  • Cyclic Nucleotide Phosphodiesterases, Type 6 / chemistry*
  • Cyclic Nucleotide Phosphodiesterases, Type 6 / genetics
  • Cyclic Nucleotide Phosphodiesterases, Type 6 / metabolism*
  • Eye Proteins / chemistry*
  • Eye Proteins / genetics
  • Eye Proteins / metabolism*
  • Models, Molecular
  • Peptide Fragments / analysis
  • Protein Binding
  • Protein Conformation
  • Protein Multimerization
  • Retina / drug effects
  • Retina / enzymology*
  • Tandem Mass Spectrometry


  • Cross-Linking Reagents
  • Eye Proteins
  • Peptide Fragments
  • Cyclic Nucleotide Phosphodiesterases, Type 6