Nucleotide-binding mechanisms in pseudokinases

Abstract

Pseudokinases are classified by the lack of one or several of the highly conserved motifs involved in nucleotide (nt) binding or catalytic activity of protein kinases (PKs). Pseudokinases represent ∼10% of the human kinome and they are found in all evolutionary classes of kinases. It has become evident that pseudokinases, which were initially considered somewhat peculiar dead kinases, are important components in several signalling cascades. Furthermore, several pseudokinases have been linked to human diseases, particularly cancer, which is raising interest for therapeutic approaches towards these proteins. The ATP-binding pocket is a well-established drug target and elucidation of the mechanism and properties of nt binding in pseudokinases is of significant interest and importance. Recent studies have demonstrated that members of the pseudokinase family are very diverse in structure as well as in their ability and mechanism to bind nts or perform phosphoryl transfer reactions. This diversity also precludes prediction of pseudokinase function, or the importance of nt binding for said function, based on primary sequence alone. Currently available data indicate that ∼40% of pseudokinases are able to bind nts, whereas only few are able to catalyse occasional phosphoryl transfer. Pseudokinases employ diverse mechanisms to bind nts, which usually occurs at low, but physiological, affinity. ATP binding serves often a structural role but in most cases the functional roles are not precisely known. In the present review, we discuss the various mechanisms that pseudokinases employ for nt binding and how this often low-affinity binding can be accurately analysed.

STK40 Is a Pseudokinase that Binds the E3 Ubiquitin Ligase COP1

“…Approximately 10% of proteins containing kinase homology domains are predicted to be enzymatically inactive (pseudokinases), owing to the absence of at least one of the conserved motifs required for efficient ATP binding or catalysis. Nearly half of these pseudokinases are reported to bind ATP, but the functional role of nucleotide binding in such cases remains unknown (Hammaren et al, 2016; Manning et al, 2002). …”

The crystal structure of PknI from Mycobacterium tuberculosis shows an inactive, pseudokinase‐like conformation

“…Additionally, one calcium ion is coordinated by Asn142 in the catalytic loop, Asp159 in the DFG motif and one water molecule that also contacts both ADP phosphates. Notably, this one cation binding mode is the most common nucleotide binding mode found among pseudokinases structures, first seen in human epidermal growth factor family pseudokinase HER3 (PDB: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4RIW) . Further, the Gly‐rich loop of PknI, which in contrast to most ePKs contains a non‐Gly residue in position 21, does not establish hydrogen bonds with the phosphates of ADP, found displaced out of the active site (Fig.…”

“…Notably, ADP binds to PknI by the one cation binding mode commonly found in eukaryotic pseudokinases ( Fig. 6A) [23], and would place the ATP c-phosphate far away from the catalytic loop ( Figs 1C and 6B). Moreover, the catalytic loop of PknI includes residue Asn139 that corresponds to the catalytic lysine Lys168 in PKA (Fig.…”

Breakthroughs in modern cancer therapy and elusive cardiotoxicity: Critical research‐practice gaps, challenges, and insights

“…104,165 Thus, the field remains largely unexplored in the research of numerous undiscovered kinases, their respective inhibitors, and their potential cardiotoxicity/toxicities. Moreover, approximately 10-20% of the kinases are classified as pseudokinases 109,166 because of the lack of one or several of the highly conserved motifs involved in nucleotide (nt) binding or catalytic activity of protein kinases. 110,165,166 Many pseudokinases in the kinome have evolved from active kinases by obtaining regulatory functions in which catalytic function is dispensable; however, a significant proportion of pseudokinases have retained their ATP-binding ability.…”

“…110,165,166 Many pseudokinases in the kinome have evolved from active kinases by obtaining regulatory functions in which catalytic function is dispensable; however, a significant proportion of pseudokinases have retained their ATP-binding ability. 166 An important molecular property of pseudokinases is that they serve as allosteric regulators of signaling pathways. 109 Pseudokinases also play an important regulatory role in cellular signaling, and the abnormal function of several human pseudokinases has been associated with human diseases, including cancers.…”