3JWR

Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with 3-isobutyl-1-methylxanthine (IBMX) and PDE6 gamma-subunit inhibitory peptide 70-87.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.994 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit

Barren, B.Gakhar, L.Muradov, H.Boyd, K.K.Ramaswamy, S.Artemyev, N.O.

(2009) Embo J. 28: 3613-3622

  • DOI: 10.1038/emboj.2009.284
  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera
A, B
330Homo sapiensMutation(s): 0 
Gene Names: PDE5A (PDE5), PDE6C (PDEA2)
EC: 3.1.4.35 3.1.4.35
Find proteins for O76074 (Homo sapiens)
Go to Gene View: PDE5A
Go to UniProtKB:  O76074
Find proteins for P51160 (Homo sapiens)
Go to Gene View: PDE6C
Go to UniProtKB:  P51160
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
C, D
18Homo sapiensMutation(s): 0 
Gene Names: PDE6G (PDEG)
EC: 3.1.4.35
Find proteins for P18545 (Homo sapiens)
Go to Gene View: PDE6G
Go to UniProtKB:  P18545
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IBM
Query on IBM

Download SDF File 
Download CCD File 
A, B
3-ISOBUTYL-1-METHYLXANTHINE
C10 H14 N4 O2
APIXJSLKIYYUKG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IBMKi: 8.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.994 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.257α = 90.00
b = 125.651β = 90.00
c = 153.854γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
d*TREKdata reduction
d*TREKdata scaling
PHENIXrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-01
    Type: Refinement description