4KU8

Structures of PKGI Reveal a cGMP-Selective Activation Mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.994 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Cyclic-Nucleotide Selectivity and cGMP-Selective Activation of PKG I.

Huang, G.Y.Kim, J.J.Reger, A.S.Lorenz, R.Moon, E.W.Zhao, C.Casteel, D.E.Bertinetti, D.Vanschouwen, B.Selvaratnam, R.Pflugrath, J.W.Sankaran, B.Melacini, G.Herberg, F.W.Kim, C.

(2014) Structure 22: 116-124

  • DOI: 10.1016/j.str.2013.09.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclic guanosine monophosphate (cGMP) and cyclic AMP (cAMP)-dependent protein kinases (PKG and PKA) are closely related homologs, and the cyclic nucleotide specificity of each kinase is crucial for keeping the two signaling pathways segregated, but t ...

    Cyclic guanosine monophosphate (cGMP) and cyclic AMP (cAMP)-dependent protein kinases (PKG and PKA) are closely related homologs, and the cyclic nucleotide specificity of each kinase is crucial for keeping the two signaling pathways segregated, but the molecular mechanism of cyclic nucleotide selectivity is unknown. Here, we report that the PKG Iβ C-terminal cyclic nucleotide binding domain (CNB-B) is highly selective for cGMP binding, and we have solved crystal structures of CNB-B with and without bound cGMP. These structures, combined with a comprehensive mutagenic analysis, allowed us to identify Leu296 and Arg297 as key residues that mediate cGMP selectivity. In addition, by comparing the cGMP bound and unbound structures, we observed large conformational changes in the C-terminal helices in response to cGMP binding, which were stabilized by recruitment of Tyr351 as a "capping residue" for cGMP. The observed rearrangements of the C-terminal helices provide a mechanical insight into release of the catalytic domain and kinase activation.


    Organizational Affiliation

    Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Building 6R2100, Berkeley, CA 94720, USA.,Department of Biochemistry, University of Kassel, Kassel 34132, Germany.,Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Chemistry, Rice University, Houston, TX 77005, USA.,Rigaku Americas, The Woodlands, TX 77381, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: ckim@bcm.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-dependent Protein Kinase 1
A, B, C
153Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

Download SDF File 
Download CCD File 
A, B
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.994 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.766α = 90.00
b = 78.766β = 90.00
c = 147.001γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-01-29
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description