Structural Basis for the Non-catalytic Functions of Protein Kinases

Abstract

Summary Protein kinases are known primarily for their ability to phosphorylate protein substrates, which constitutes an essential biological process. Recently, compelling evidence has accumulated that the functions of many protein kinases extend beyond phosphorylation and include an impressive spectrum of non-catalytic roles, such as scaffolding, allosteric regulation, or even protein-DNA interactions. How the conserved kinase fold shared by all metazoan protein kinases can accomplish these diverse tasks in a specific and regulated manner is poorly understood. In this review, we analyze the molecular mechanisms supporting phosphorylation-independent signaling by kinases and attempt to identify common and unique structural characteristics that enable kinases to perform non-catalytic functions. We also discuss how post-translational modifications, protein-protein interactions, and small molecules modulate these non-canonical kinase functions. Finally, we highlight current efforts in the targeted design of small molecule modulators of non-catalytic kinase functions – a new pharmacological challenge for which structural considerations are more important than ever.

Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity

“…However, our results argue against the canonical protein kinase model and instead support an unorthodox protein kinase-like (uPKL) functionality for COQ8 (referring to both mammalian COQ8A/B and yeast Coq8p, which we propose to function through the same fundamental mechanisms). Thus, our work adds COQ8 to an expanding list of PKL superfamily members with non-canonical activities that are central to their biological functions (Kung and Jura, 2016). …”

“…Unorthodox PKL functions, including lipid kinase activity (Walker et al, 1999) and nucleotide-regulated conformational changes (Kung and Jura, 2016), are increasingly recognized. Moreover, 10% of the human kinome consists of pseudokinases with non-catalytic functions (Zeqiraj and van Aalten, 2010).…”

cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility–mass spectrometry

“…Interestingly, the preferential targeting of ‘type II’ kinase inhibitor classes to inactive kinase conformers of tyrosine kinases is well known and clinically relevant [43,51]. However, the propensity of inactive Ser/Thr kinases, exemplified by K72H PKAc (the present study) or multiple pseudokinases [47], to bind to different classes of kinase inhibitor is an important new area of research focus [70,79,80]. Our work demonstrates that, for an unphosphorylated K72H PKAc mutant, an inability to bind to ATP does not preclude binding to bisindole-based ATP-competitive inhibitors whose lack of specificity precludes their rational exploitation as chemical biology probe compounds [19].…”

The evolving world of pseudoenzymes: proteins, prejudice and zombies

“…We have already mentioned that catalytically active enzymes can also serve important functions as modulators of signalling through non-catalytic functions [12, 13]. This leads us to believe that enzyme structures are predisposed to mediating interactions with protein or metabolite ligands and thus these folds are the ideal templates for nature to repurpose for entirely new functions (Figs.…”

“…Recent studies support the idea that insights from studies of pseudoenzymes can provide a window into understanding the non-catalytic functions of conventional enzymes [12, 13, 19]. On the whole, it is conformation (rather than catalytic output) that is most critical for the regulated activation and inactivation cycles that most enzymes undergo as part of homeostatic mechanisms.…”