5J48

PKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-pCPT-cGMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Analog Specificity in PKG I and II.

Campbell, J.C.Henning, P.Franz, E.Sankaran, B.Herberg, F.W.Kim, C.

(2017) ACS Chem. Biol. 12: 2388-2398

  • DOI: 10.1021/acschembio.7b00369
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclic GMP analogs, 8-Br, 8-pCPT, and PET-cGMP, have been widely used for characterizing cellular functions of cGMP-dependent protein kinase (PKG) I and II isotypes. However, interpreting results obtained using these analogs has been difficult due to ...

    Cyclic GMP analogs, 8-Br, 8-pCPT, and PET-cGMP, have been widely used for characterizing cellular functions of cGMP-dependent protein kinase (PKG) I and II isotypes. However, interpreting results obtained using these analogs has been difficult due to their low isotype specificity. Additionally, each isotype has two binding sites with different cGMP affinities and analog selectivities, making understanding the molecular basis for isotype specificity of these compounds even more challenging. To determine isotype specificity of cGMP analogs and their structural basis, we generated the full-length regulatory domains of PKG I and II isotypes with each binding site disabled, determined their affinities for these analogs, and obtained cocrystal structures of both isotypes bound with cGMP analogs. Our affinity and activation measurements show that PET-cGMP is most selective for PKG I, whereas 8-pCPT-cGMP is most selective for PKG II. Our structures of cyclic nucleotide binding (CNB) domains reveal that the B site of PKG I is more open and forms a unique π/π interaction through Arg285 at β4 with the PET moiety, whereas the A site of PKG II has a larger β5/β6 pocket that can better accommodate the bulky 8-pCPT moiety. Our structural and functional results explain the selectivity of these analogs for each PKG isotype and provide a starting point for the rational design of isotype selective activators.


    Organizational Affiliation

    Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine , Houston, Texas, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , Houston, Texas, United States.,Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory , Berkeley, California, United States.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine , Houston, Texas, United States.,Department of Biochemistry, University of Kassel , Kassel, Hesse, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-dependent protein kinase 1
A, B
135Homo sapiensMutation(s): 0 
Gene Names: PRKG1 (PRKG1B, PRKGR1A, PRKGR1B)
EC: 2.7.11.12
Find proteins for Q13976 (Homo sapiens)
Go to Gene View: PRKG1
Go to UniProtKB:  Q13976
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6FW
Query on 6FW

Download SDF File 
Download CCD File 
A, B
2-amino-8-[(4-chlorophenyl)sulfanyl]-9-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-3,9-dihydro-6H-purin-6-one
C16 H15 Cl N5 O7 P S
ZDJHIEHUVPCEDK-IDTAVKCVSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.510α = 90.00
b = 59.240β = 100.17
c = 67.320γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
PHENIXphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Database references