Co-crystal structure of PKA RI alpha CNB-B mutant (G316R/A336T) with cAMP

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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This is version 1.6 of the entry. See complete history


Mutations of PKA cyclic nucleotide-binding domains reveal novel aspects of cyclic nucleotide selectivity.

Lorenz, R.Moon, E.W.Kim, J.J.Schmidt, S.H.Sankaran, B.Pavlidis, I.V.Kim, C.Herberg, F.W.

(2017) Biochem J 474: 2389-2403

  • DOI: https://doi.org/10.1042/BCJ20160969
  • Primary Citation of Related Structures:  
    5KJX, 5KJY, 5KJZ

  • PubMed Abstract: 

    Cyclic AMP and cyclic GMP are ubiquitous second messengers that regulate the activity of effector proteins in all forms of life. The main effector proteins, the 3',5'-cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) and the 3',5'-cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG), are preferentially activated by cAMP and cGMP, respectively. However, the molecular basis of this cyclic nucleotide selectivity is still not fully understood. Analysis of isolated cyclic nucleotide-binding (CNB) domains of PKA regulatory subunit type Iα (RIα) reveals that the C-terminal CNB-B has a higher cAMP affinity and selectivity than the N-terminal CNB-A. Here, we show that introducing cGMP-specific residues using site-directed mutagenesis reduces the selectivity of CNB-B, while the combination of two mutations (G316R/A336T) results in a cGMP-selective binding domain. Furthermore, introducing the corresponding mutations (T192R/A212T) into the PKA RIα CNB-A turns this domain into a highly cGMP-selective domain, underlining the importance of these contacts for achieving cGMP specificity. Binding data with the generic purine nucleotide 3',5'-cyclic inosine monophosphate (cIMP) reveal that introduced arginine residues interact with the position 6 oxygen of the nucleobase. Co-crystal structures of an isolated CNB-B G316R/A336T double mutant with either cAMP or cGMP reveal that the introduced threonine and arginine residues maintain their conserved contacts as seen in PKG I CNB-B. These results improve our understanding of cyclic nucleotide binding and the molecular basis of cyclic nucleotide specificity.

  • Organizational Affiliation

    Department of Biochemistry, University of Kassel, Kassel, Hesse, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase type I-alpha regulatory subunit150Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P10644 (Homo sapiens)
Explore P10644 
Go to UniProtKB:  P10644
PHAROS:  P10644
GTEx:  ENSG00000108946 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10644
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CMP

Download Ideal Coordinates CCD File 
C10 H12 N5 O6 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.7α = 90
b = 98.7β = 90
c = 36.17γ = 120
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Federal Ministry of Education and Research GrantGermanyFKZ 0316177F (No Pain)
The Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) of the University of KasselGermany--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R01GM090161-06

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Structure summary
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description