Crystal structure of cAMP bound cGMP-dependent protein kinase(92-227)

Experimental Data Snapshot

  • Resolution: 2.49 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Co-Crystal Structures of PKG Ibeta (92-227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding

Kim, J.J.Casteel, D.E.Huang, G.Kwon, T.H.Ren, R.K.Zwart, P.Headd, J.J.Brown, N.G.Chow, D.C.Palzkill, T.Kim, C.

(2011) PLoS One 6: e18413-e18413

  • DOI: https://doi.org/10.1371/journal.pone.0018413
  • Primary Citation of Related Structures:  
    3OCP, 3OD0, 3OGJ

  • PubMed Abstract: 

    Cyclic GMP-dependent protein kinases (PKGs) are central mediators of the NO-cGMP signaling pathway and phosphorylate downstream substrates that are crucial for regulating smooth muscle tone, platelet activation, nociception and memory formation. As one of the main receptors for cGMP, PKGs mediate most of the effects of cGMP elevating drugs, such as nitric oxide-releasing agents and phosphodiesterase inhibitors which are used for the treatment of angina pectoris and erectile dysfunction, respectively. We have investigated the mechanism of cyclic nucleotide binding to PKG by determining crystal structures of the amino-terminal cyclic nucleotide-binding domain (CNBD-A) of human PKG I bound to either cGMP or cAMP. We also determined the structure of CNBD-A in the absence of bound nucleotide. The crystal structures of CNBD-A with bound cAMP or cGMP reveal that cAMP binds in either syn or anti configurations whereas cGMP binds only in a syn configuration, with a conserved threonine residue anchoring both cyclic phosphate and guanine moieties. The structure of CNBD-A in the absence of bound cyclic nucleotide was similar to that of the cyclic nucleotide bound structures. Surprisingly, isothermal titration calorimetry experiments demonstrated that CNBD-A binds both cGMP and cAMP with a relatively high affinity, showing an approximately two-fold preference for cGMP. Our findings suggest that CNBD-A binds cGMP in the syn conformation through its interaction with Thr193 and an unusual cis-peptide forming residues Leu172 and Cys173. Although these studies provide the first structural insights into cyclic nucleotide binding to PKG, our ITC results show only a two-fold preference for cGMP, indicating that other domains are required for the previously reported cyclic nucleotide selectivity.

  • Organizational Affiliation

    Department of Pharmacology, Baylor College of Medicine, Houston, Texas, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PRKG1 protein
A, B
139Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13976 (Homo sapiens)
Explore Q13976 
Go to UniProtKB:  Q13976
GTEx:  ENSG00000185532 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13976
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CMP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C10 H12 N5 O6 P
Binding Affinity Annotations 
IDSourceBinding Affinity
CMP PDBBind:  3OCP Kd: 27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.49 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.139α = 90
b = 107.139β = 90
c = 168.967γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description