cAMP-dependent protein kinase (PKA), ubiquitous in mammalian cells, regulates a plethora of cell processes including development, differentiation, memory, and metabolism and is associated with many diseases including multiple endocrine disorders and cancer. It serves as a prototype for the protein kinase superfamily and its activation by cAMP is a classic example of allosteric regulation. While our studies of PKA structure and function have given us a molecular understanding of individual PKA catalytic and regulatory subunits, over the past four years we have added a new dimension to our understanding of PKA signaling by solving structures of PKA tetrameric holoenzymes. These first glimpses of the full-length proteins force us to appreciate that PKA functions as a complex and multicomponent signaling system. Protein kinases have evolved to be dynamic and highly regulated molecular switches, not efficient catalysts, and we simply cannot appreciate or understand how this PKA signaling system works and how it is allosterically regulated by cAMP without seeing the full-length holoenzymes. It is these large multi-domain tetrameric complexes that represent the physiological state of PKA signaling in cells, and the quaternary structure of each isoform (RI?, RI?, RII?, and RII?) is different, as we had predicted based on our low resolution SAXS analyses. Our goals now are to further define the molecular features of these holoenzymes as integrated and finely tuned systems using RI? and RII? holoenzymes as prototypical isoforms that nucleate dynamic multicomponent macromolecular PKA signaling complexes.
Aim I focuses on RI? and uses a disease mutation of RI? to dissect the pathway for allosteric signaling from one cAMP-binding domain to the other. Crystal structures of the full-length mutant holoenzyme will be validated using solution methods such as SAXS and SANS while mutagenesis will confirm interfaces and provide functional, mechanistic insights. To build higher levels of RI? complexity we focus on two newly discovered proteins. P-Rex1, up-regulated in cancers, is a guanine nucleotide exchange factor for Rac1 that binds through its two PDZ domains to the C-terminal PDZ motif of RI?. To the N-terminal D/D domain we are adding a small newly discovered membrane associated RI-specific AKAP, smAKAP.
In Aim II we are building a quantitative model for PKA signaling by RII?. We specifically define the role of phosphatases, metals (both Mg2+ and Ca2+), and phosphodiesterases. We introduce new concepts by showing the importance of the turnover of a single phosphate in RII? and emphasize that the release of cAMP from RII? is not diffusion limited. Finally, in Aim III we build higher levels of complexity for the RII? "signalosome" by adding a dual-specific AKAP, DAKAP2, to the holoenzyme. DAKAP2 is a multi-domain AKAP that regulates recycling by binding through its PDZ motif to PDZ-K1, which links it to transporters, and through its RGS domains that bind to Rabs. In parallel with crystallography, we will use small angle Xray and neutron scattering as well as single particle image reconstruction to monitor conformational changes and domain organization in solution.

Public Health Relevance

Cyclic AMP-dependent protein kinase (PKA), ubiquitous in mammalian cells and associated with many diseases, including cancers, is assembled as a macromolecular complex at specific sites in the cell where it regulates functions such as memory, cell migration, differentiation, and metabolism. Here we are defining the molecular and dynamic features of this signaling system that is nucleated in an isoform specific way by the regulatory and catalytic subunits of PKA at high resolution by crystallography and at low resolution using solution methods that include small angle X-ray and neutron scattering and single particle EM imaging. A final goal is to create a quantitative model of the PKA signaling system.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
2R01GM034921-29A1
Application #
8762152
Study Section
Molecular and Integrative Signal Transduction Study Section (MIST)
Program Officer
Gerratana, Barbara
Project Start
Project End
Budget Start
Budget End
Support Year
29
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California San Diego
Department
Pharmacology
Type
Schools of Medicine
DUNS #
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Bruystens, Jessica Gh; Wu, Jian; Fortezzo, Audrey et al. (2016) Structure of a PKA RIα Recurrent Acrodysostosis Mutant Explains Defective cAMP-Dependent Activation. J Mol Biol 428:4890-4904
Chávez-Vargas, Lydia; Adame-García, Sendi Rafael; Cervantes-Villagrana, Rodolfo Daniel et al. (2016) Protein Kinase A (PKA) Type I Interacts with P-Rex1, a Rac Guanine Nucleotide Exchange Factor: EFFECT ON PKA LOCALIZATION AND P-Rex1 SIGNALING. J Biol Chem 291:6182-99
Burgers, Pepijn P; Bruystens, Jessica; Burnley, Rebecca J et al. (2016) Structure of smAKAP and its regulation by PKA-mediated phosphorylation. FEBS J 283:2132-48
Zhang, Ping; Knape, Matthias J; Ahuja, Lalima G et al. (2015) Single Turnover Autophosphorylation Cycle of the PKA RIIβ Holoenzyme. PLoS Biol 13:e1002192
Sarma, Ganapathy N; Moody, Issa S; Ilouz, Ronit et al. (2015) D-AKAP2:PKA RII:PDZK1 ternary complex structure: insights from the nucleation of a polyvalent scaffold. Protein Sci 24:105-16
Akimoto, Madoka; McNicholl, Eric Tyler; Ramkissoon, Avinash et al. (2015) Mapping the Free Energy Landscape of PKA Inhibition and Activation: A Double-Conformational Selection Model for the Tandem cAMP-Binding Domains of PKA RIα. PLoS Biol 13:e1002305
Zhang, Ping; Ye, Feng; Bastidas, Adam C et al. (2015) An Isoform-Specific Myristylation Switch Targets Type II PKA Holoenzymes to Membranes. Structure 23:1563-72
Zhang, Ping; Kornev, Alexandr P; Wu, Jian et al. (2015) Discovery of Allostery in PKA Signaling. Biophys Rev 7:227-238
Malmstrom, Robert D; Kornev, Alexandr P; Taylor, Susan S et al. (2015) Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nat Commun 6:7588
Bruystens, Jessica G H; Wu, Jian; Fortezzo, Audrey et al. (2014) PKA RIα homodimer structure reveals an intermolecular interface with implications for cooperative cAMP binding and Carney complex disease. Structure 22:59-69

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