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      There’s more to death than life: Noncatalytic functions in kinase and pseudokinase signaling

      review-article
      1 , , 2 , 3 ,
      The Journal of Biological Chemistry
      American Society for Biochemistry and Molecular Biology
      pseudoenzyme, dead enzyme, nonenzyme, protein kinase, protein structure, BUBR1, BUB1 related-1, DSF, differential scanning fluorimetry, EGFR, epidermal growth factor receptor, HDX-MS, hydrogen-deuterium exchange mass spectrometry, HER, Receptor tyrosine-protein kinase erbB, ILK, integrin-linked kinase, IRAK, IL-1 receptor-associated kinase, JAK, Janus kinase, KSR, kinase suppressor of Ras, MEK1, MAPK/ERK kinase 1, MLKL, mixed lineage kinase domain-like, PABPs, poly(A)-binding proteins, PEAK, pseudopodium-enriched atypical kinase, PK-1, protein kinase-1, PsK, pseudokinase, RAF, rapidly accelerated fibrosarcoma kinase, RIPK, receptor interacting serine/threonine kinase, RKS1, resistance-related kinase 1, SgK, Sugen kinase, TRIB, Tribbles family pseudokinase, ULK4, Unc-51-like kinase 4

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          Abstract

          Protein kinases are present in all domains of life and play diverse roles in cellular signaling. Whereas the impact of substrate phosphorylation by protein kinases has long been appreciated, it is becoming increasingly clear that protein kinases also play other, noncatalytic, functions. Here, we review recent developments in understanding the noncatalytic functions of protein kinases. Many noncatalytic activities are best exemplified by protein kinases that are devoid of enzymatic activity altogether—known as pseudokinases. These dead proteins illustrate that, beyond conventional notions of kinase function, catalytic activity can be dispensable for biological function. Through key examples we illustrate diverse mechanisms of noncatalytic kinase activity: as allosteric modulators; protein-based switches; scaffolds for complex assembly; and as competitive inhibitors in signaling pathways. In common, these noncatalytic mechanisms exploit the nature of the protein kinase fold as a versatile protein–protein interaction module. Many examples are also intrinsically linked to the ability of the protein kinase to switch between multiple states, a function shared with catalytic protein kinases. Finally, we consider the contemporary landscape of small molecules to modulate noncatalytic functions of protein kinases, which, although challenging, has significant potential given the scope of noncatalytic protein kinase function in health and disease.

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          Most cited references109

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          The protein kinase complement of the human genome.

          G. Manning (2002)
          We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.
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            Protein kinases: evolution of dynamic regulatory proteins.

            Eukayotic protein kinases evolved as a family of highly dynamic molecules with strictly organized internal architecture. A single hydrophobic F-helix serves as a central scaffold for assembly of the entire molecule. Two non-consecutive hydrophobic structures termed "spines" anchor all the elements important for catalysis to the F-helix. They make firm, but flexible, connections within the molecule, providing a high level of internal dynamics of the protein kinase. During the course of evolution, protein kinases developed a universal regulatory mechanism associated with a large activation segment that can be dynamically folded and unfolded in the course of cell functioning. Protein kinases thus represent a unique, highly dynamic, and precisely regulated set of switches that control most biological events in eukaryotic cells. Copyright © 2010. Published by Elsevier Ltd.
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              The protein kinase family: conserved features and deduced phylogeny of the catalytic domains.

              In recent years, members of the protein kinase family have been discovered at an accelerated pace. Most were first described, not through the traditional biochemical approach of protein purification and enzyme assay, but as putative protein kinase amino acid sequences deduced from the nucleotide sequences of molecularly cloned genes or complementary DNAs. Phylogenetic mapping of the conserved protein kinase catalytic domains can serve as a useful first step in the functional characterization of these newly identified family members.
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                Author and article information

                Contributors
                Journal
                J Biol Chem
                J Biol Chem
                The Journal of Biological Chemistry
                American Society for Biochemistry and Molecular Biology
                0021-9258
                1083-351X
                22 April 2021
                2021
                22 April 2021
                : 296
                : 100705
                Affiliations
                [1 ]Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
                [2 ]Inflammation Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
                [3 ]Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
                Author notes
                []For correspondence: Peter D. Mace; James M. Murphy peter.mace@ 123456otago.ac.nz jamesm@ 123456wehi.edu.au
                Article
                S0021-9258(21)00494-4 100705
                10.1016/j.jbc.2021.100705
                8141879
                33895136
                8526f5ea-e91e-498a-a83c-cc81d3277835
                © 2021 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 15 March 2021
                : 20 April 2021
                Categories
                JBC Reviews

                Biochemistry
                pseudoenzyme,dead enzyme,nonenzyme,protein kinase,protein structure,bubr1, bub1 related-1,dsf, differential scanning fluorimetry,egfr, epidermal growth factor receptor,hdx-ms, hydrogen-deuterium exchange mass spectrometry,her, receptor tyrosine-protein kinase erbb,ilk, integrin-linked kinase,irak, il-1 receptor-associated kinase,jak, janus kinase,ksr, kinase suppressor of ras,mek1, mapk/erk kinase 1,mlkl, mixed lineage kinase domain-like,pabps, poly(a)-binding proteins,peak, pseudopodium-enriched atypical kinase,pk-1, protein kinase-1,psk, pseudokinase,raf, rapidly accelerated fibrosarcoma kinase,ripk, receptor interacting serine/threonine kinase,rks1, resistance-related kinase 1,sgk, sugen kinase,trib, tribbles family pseudokinase,ulk4, unc-51-like kinase 4

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