There’s more to death than life: Noncatalytic functions in kinase and pseudokinase signaling
2021; Elsevier BV; Volume: 296; Linguagem: Inglês
10.1016/j.jbc.2021.100705
ISSN1083-351X
AutoresPeter D. Mace, James M. Murphy,
Tópico(s)Endoplasmic Reticulum Stress and Disease
ResumoProtein 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. 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. Protein kinases are quintessential signaling proteins. Their ability to posttranslationally modify amino acid side chains with a phosphoryl group underlies a broad swath of eukaryotic biology (1Hardman G. Perkins S. Brownridge P.J. Clarke C.J. Byrne D.P. Campbell A.E. Kalyuzhnyy A. Myall A. Eyers P.A. Jones A.R. Eyers C.E. Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation.EMBO J. 2019; 38e100847Crossref PubMed Scopus (31) Google Scholar) and regulates protein activity in diverse pathways. In addition to catalyzing phosphoryl transfer, protein kinases also function in noncatalytic roles, interacting with other proteins and modifying their activity. A significant proportion of kinases even take noncatalytic function to the extreme—lacking phosphoryl-transfer activity completely—and are known as pseudokinases (2Manning G. Whyte D.B. Martinez R. Hunter T. Sudarsanam S. The protein kinase complement of the human genome.Science. 2002; 298: 1912-1934Crossref PubMed Scopus (5717) Google Scholar, 3Zeqiraj E. van Aalten D.M.F. Pseudokinases-remnants of evolution or key allosteric regulators?.Curr. Opin. Struct. Biol. 2010; 20: 772-781Crossref PubMed Scopus (102) Google Scholar, 4Eyers P.A. Murphy J.M. Dawn of the dead: Protein pseudokinases signal new adventures in cell biology.Biochem. Soc. Trans. 2013; 41: 969-974Crossref PubMed Scopus (60) Google Scholar). Originally thought to be dead evolutionary remnants, pseudokinases have since been revealed to play remarkably diverse noncatalytic roles in biological pathways (5Jacobsen A.V. Murphy J.M. The secret life of kinases: Insights into non-catalytic signalling functions from pseudokinases.Biochem. Soc. Trans. 2017; 45: 665-681Crossref PubMed Scopus (41) Google Scholar). Importantly, these zombie proteins provide a window into understanding the often unheralded, nonenzymatic functions that can be performed by their alive enzyme counterparts. Catalytically competent protein kinases are diverse, but their shared enzymatic activity means that their protein folds are similar and core catalytic elements show little variation (Fig. 1A). The key elements for protein kinase catalysis are the ability to bind ATP, coordinate Mg2+, and catalyze phosphoryl transfer. These core elements generally consist of: a lysine residue within the VAIK motif in the N-terminal lobe, and a glycine rich loop (Gly-loop), which are key features for enabling ATP binding; an aspartate from the DFG-motif in the activation loop that coordinates magnesium alongside ATP; and an aspartate from the HRD loop contributed from the C-terminal lobe, which acts as a catalytic base during phosphoryl transfer (Fig. 1B; (2Manning G. Whyte D.B. Martinez R. Hunter T. Sudarsanam S. The protein kinase complement of the human genome.Science. 2002; 298: 1912-1934Crossref PubMed Scopus (5717) Google Scholar, 6Hanks S.K. Quinn A.M. Hunter T. The protein kinase family: Conserved features and deduced phylogeny of the catalytic domains.Science. 1988; 241: 42-52Crossref PubMed Google Scholar)). Any, or multiple, of these elements can be lost in pseudokinases (7Kung J.E. Jura N. Prospects for pharmacological targeting of pseudokinases.Nat. Rev. Drug Discov. 2019; 18: 501-526Crossref PubMed Scopus (28) Google Scholar, 8Kwon A. Scott S. Taujale R. Yeung W. Kochut K.J. Eyers P.A. Kannan N. Tracing the origin and evolution of pseudokinases across the tree of life.Sci. Signal. 2019; 12eaav3810Crossref PubMed Scopus (28) Google Scholar, 9Murphy J.M. Zhang Q. Young S.N. Reese M.L. Bailey F.P. Eyers P.A. Ungureanu D. Hammarén H. Silvennoinen O. Varghese L.N. Chen K. Tripaydonis A. Jura N. Fukuda K. Qin J. et al.A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties.Biochem. J. 2014; 457: 323-334Crossref PubMed Scopus (0) Google Scholar). Depending on what elements are lost, pseudokinases may be unable to bind nucleotides or magnesium (Class I), bind nucleotides but not cations (Class II), bind cations only (Class III), or bind both nucleotides and cations, but are still unable to carry out phosphoryl transfer (Class IV) (Fig. 1C) (9Murphy J.M. Zhang Q. Young S.N. Reese M.L. Bailey F.P. Eyers P.A. Ungureanu D. Hammarén H. Silvennoinen O. Varghese L.N. Chen K. Tripaydonis A. Jura N. Fukuda K. Qin J. et al.A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties.Biochem. J. 2014; 457: 323-334Crossref PubMed Scopus (0) Google Scholar). Analyses of protein coding genes across archaea, bacteria, and eukaryotes have identified protein kinases, and pseudokinases, in all domains (8Kwon A. Scott S. Taujale R. Yeung W. Kochut K.J. Eyers P.A. Kannan N. Tracing the origin and evolution of pseudokinases across the tree of life.Sci. Signal. 2019; 12eaav3810Crossref PubMed Scopus (28) Google Scholar). This review focuses on the eukaryotic protein kinase fold, which is predicted to be present in low abundance in archaea and bacteria (10Childers W.S. Shapiro L. A pseudokinase couples signaling pathways to enable asymmetric cell division in a bacterium.Microb. Cell. 2014; 2: 29-32Crossref PubMed Scopus (0) Google Scholar, 11Gee C.L. Papavinasasundaram K.G. Blair S.R. Baer C.E. Falick A.M. King D.S. Griffin J.E. Venghatakrishnan H. Zukauskas A. Wei J.-R. Dhiman R.K. Crick D.C. Rubin E.J. Sassetti C.M. Alber T. A phosphorylated pseudokinase complex controls cell wall synthesis in mycobacteria.Sci. Signal. 2012; 5ra7Crossref PubMed Scopus (0) Google Scholar), although our understanding of protein kinases more broadly in prokaryotes is still emerging (12Kannan N. Taylor S.S. Zhai Y. Venter J.C. Manning G. Structural and functional diversity of the microbial kinome.PLoS Biol. 2007; 5e17Crossref PubMed Scopus (195) Google Scholar, 13Pérez J. Castañeda-García A. Jenke-Kodama H. Müller R. Muñoz-Dorado J. Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome.Proc. Natl. Acad. Sci. U. S. A. 2008; 105: 15950-15955Crossref PubMed Scopus (83) Google Scholar). The human proteome has long been known to contain approximately 550 protein kinases, of which approximately 10% are pseudokinases. This proportion of noncatalytic kinases is generally retained across vertebrates, with approximately ∼10% of protein kinomes designated as pseudokinases (2Manning G. Whyte D.B. Martinez R. Hunter T. Sudarsanam S. The protein kinase complement of the human genome.Science. 2002; 298: 1912-1934Crossref PubMed Scopus (5717) Google Scholar, 14Caenepeel S. Charydczak G. Sudarsanam S. Hunter T. Manning G. The mouse kinome: Discovery and comparative genomics of all mouse protein kinases.Proc. Natl. Acad. Sci. U. S. A. 2004; 101: 11707-11712Crossref PubMed Scopus (237) Google Scholar). More broadly, some eukaryotic species have expanded pseudokinase complements. For instance, the kinomes of plants frequently comprise up to ∼17% pseudokinases, and approximately half of kinase-like proteins in selected protists (Toxoplasma gondii and Giardia lamblia) lack essential catalytic residues (8Kwon A. Scott S. Taujale R. Yeung W. Kochut K.J. Eyers P.A. Kannan N. Tracing the origin and evolution of pseudokinases across the tree of life.Sci. Signal. 2019; 12eaav3810Crossref PubMed Scopus (28) Google Scholar). Such pseudokinase expansion is frequently concentrated in specific classes of kinases. For example, plants have undergone a massive expansion of pseudokinases, likely due to their important role in innate immunity (15Jubic L.M. Saile S. Furzer O.J. El Kasmi F. Dangl J.L. Help wanted: Helper NLRs and plant immune responses.Curr. Opin. Plant Biol. 2019; 50: 82-94Crossref PubMed Scopus (53) Google Scholar). The broad scale of current analyses means that most pseudokinase classification is sequence-based rather than experimentally verified. While computational approaches have been enlightening, several pertinent examples demonstrate the need to couple with experimental characterization. For instance, kinases with seemingly degraded catalytic sequences can nonetheless retain the ability to phosphorylate proteins or other specific biomolecules (16Beraki T. Hu X. Broncel M. Young J.C. O'Shaughnessy W.J. Borek D. Treeck M. Reese M.L. Divergent kinase regulates membrane ultrastructure of the Toxoplasma parasitophorous vacuole.Proc. Natl. Acad. Sci. U. S. A. 2019; 116: 6361-6370Crossref PubMed Scopus (0) Google Scholar, 17Zhu Q. Venzke D. Walimbe A.S. Anderson M.E. Fu Q. Kinch L.N. Wang W. Chen X. Grishin N.V. Huang N. Yu L. Dixon J.E. Campbell K.P. Xiao J. Structure of protein O-mannose kinase reveals a unique active site architecture.Elife. 2016; 5e22238Crossref PubMed Scopus (19) Google Scholar, 18Yoshida-Moriguchi T. Willer T. Anderson M.E. Venzke D. Whyte T. Muntoni F. Lee H. Nelson S.F. Yu L. Campbell K.P. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function.Science. 2013; 341: 896-899Crossref PubMed Scopus (139) Google Scholar, 19Lopez V.A. Park B.C. Nowak D. Sreelatha A. Zembek P. Fernandez J. Servage K.A. Gradowski M. Hennig J. Tomchick D.R. Pawłowski K. Krzymowska M. Tagliabracci V.S. A bacterial effector mimics a host HSP90 client to undermine immunity.Cell. 2019; 179: 205-218.e21Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar) or can carry out completely unanticipated catalytic functions distinct from phosphoryl transfer (20Black M.H. Osinski A. Gradowski M. Servage K.A. Pawłowski K. Tomchick D.R. Tagliabracci V.S. Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases.Science. 2019; 364: 787-792Crossref PubMed Scopus (41) Google Scholar, 21Sulpizio A. Minelli M.E. Wan M. Burrowes P.D. Wu X. Sanford E.J. Shin J.-H. Williams B.C. Goldberg M.L. Smolka M.B. Mao Y. Protein polyglutamylation catalyzed by the bacterial calmodulin-dependent pseudokinase SidJ.Elife. 2019; 8e51162Crossref PubMed Scopus (19) Google Scholar, 22Bhogaraju S. Bonn F. Mukherjee R. Adams M. Pfleiderer M.M. Galej W.P. Matkovic V. Lopez-Mosqueda J. Kalayil S. Shin D. Dikic I. Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin catalysed glutamylation.Nature. 2019; 572: 382-386Crossref PubMed Scopus (34) Google Scholar, 23Sreelatha A. Yee S.S. Lopez V.A. Park B.C. Kinch L.N. Pilch S. Servage K.A. Zhang J. Jiou J. Karasiewicz-Urbańska M. Łobocka M. Grishin N.V. Orth K. Kucharczyk R. Pawłowski K. et al.Protein AMPylation by an evolutionarily conserved pseudokinase.Cell. 2018; 175: 809-821.e19Abstract Full Text Full Text PDF PubMed Scopus (54) Google Scholar). Nonetheless, coupled bioinformatic and experimental approaches will be essential for continued insight into the conserved and important noncatalytic roles played by kinases throughout evolution. Pseudokinases have led the emerging realization that catalytically inactive enzymes (pseudoenzymes) play roles in almost all facets of biology (24Ribeiro A.J.M. Das S. Dawson N. Zaru R. Orchard S. Thornton J.M. Orengo C. Zeqiraj E. Murphy J.M. Eyers P.A. Emerging concepts in pseudoenzyme classification, evolution, and signaling.Sci. Signal. 2019; 12eaat9797Crossref PubMed Scopus (32) Google Scholar). Across protein families and kingdoms of life, proteins that have an enzymatic fold but lack catalytic activity regulate biological processes through a number of different mechanisms (24Ribeiro A.J.M. Das S. Dawson N. Zaru R. Orchard S. Thornton J.M. Orengo C. Zeqiraj E. Murphy J.M. Eyers P.A. Emerging concepts in pseudoenzyme classification, evolution, and signaling.Sci. Signal. 2019; 12eaat9797Crossref PubMed Scopus (32) Google Scholar, 25Murphy J.M. Mace P.D. Eyers P.A. Live and let die: Insights into pseudoenzyme mechanisms from structure.Curr. Opin. Struct. Biol. 2017; 47: 95-104Crossref PubMed Scopus (54) Google Scholar, 26Murphy J.M. Farhan H. Eyers P.A. Bio-zombie: The rise of pseudoenzymes in biology.Biochem. Soc. Trans. 2017; 45: 537-544Crossref PubMed Scopus (47) Google Scholar). Pseudoenzymes include pseudo-phosphatases, pseudoproteases, and pseudoGTPases, among others. Broadly speaking, pseudoenzymes function as: allosteric activators, competitive inhibitors, scaffolds for assembly of protein complexes, or as protein switches (Fig. 2; (25Murphy J.M. Mace P.D. Eyers P.A. Live and let die: Insights into pseudoenzyme mechanisms from structure.Curr. Opin. Struct. Biol. 2017; 47: 95-104Crossref PubMed Scopus (54) Google Scholar)). Examples in each of these categories show that regulatory features and interaction surfaces evolved for catalytic proteins can be retained or repurposed toward alternative biological function in noncatalytic versions of the same protein or eschewed completely to evolve new activity. Thus, while pseudoenzymes are noncatalytic, this does not mean they are nonfunctional. It is also important to note that pseudoenzymes are not the same as pseudogenes. Pseudogenes refer to incomplete DNA sequences lacking regulatory elements, whereas pseudoenzymes are translated proteins encoded by functional genes. Here, we focus on recent illustrative examples for understanding noncatalytic functions of protein kinases at the molecular level. Because they are by definition noncatalytic, pseudokinases provide many of the clearest examples of noncatalytic regulation and function across each of the known categories of pseudoenzymes. Noncatalytic kinase function is particularly linked to function as protein switches, because the core architecture of the kinase domain encodes the ability to switch between on- and off-states. Many pseudokinases have retained the ability to switch between different conformations even though they lack core catalytic elements. This means that some pseudokinases can function as switches to regulate activity, but simultaneously as scaffolds, inhibitors, or activators. Thus, when freed from the constraints of retaining enzymatic activity, protein kinases can elaborate on functions beyond catalysis or develop completely novel roles as dead enzymes. Accordingly, dead enzymes offer exemplars of additional, often unrecognized noncatalytic functions that might be performed by conventional, alive enzymes—in keeping with the idea that, at least in the case of enzymes, there is more to death than life. One of the best-characterized functions of pseudokinases is their modulation of cognate kinases, by either promoting or attenuating catalytic activity of their binding partners. Because pseudokinases have often arisen from gene duplication events, they frequently function within the same pathway as their cognate kinase partners owing to common expression patterns and subcellular localization, as noted previously (26Murphy J.M. Farhan H. Eyers P.A. Bio-zombie: The rise of pseudoenzymes in biology.Biochem. Soc. Trans. 2017; 45: 537-544Crossref PubMed Scopus (47) Google Scholar, 27Adrain C. Freeman M. New lives for old: Evolution of pseudoenzyme function illustrated by iRhoms.Nat. Rev. Mol. Cell Biol. 2012; 13: 489-498Crossref PubMed Scopus (102) Google Scholar, 28Pils B. Schultz J. Inactive enzyme-homologues find new function in regulatory processes.J. Mol. Biol. 2004; 340: 399-404Crossref PubMed Scopus (109) Google Scholar). Such duplications bring enormous liberty; because of the functional redundancy that arises within a pathway through duplication, there is no necessity to maintain active site catalytic residues or geometry to mediate phosphoryl transfer. One of the most striking examples is in the Janus Kinase (JAK) family, where a pseudokinase domain (termed JH2) occurs in tandem, N-terminal to the catalytically active tyrosine kinase domain (termed JH1) and attenuates its catalytic activity, likely in trans within receptor-scaffolded dimers (29Brooks A.J. Dai W. O'Mara M.L. Abankwa D. Chhabra Y. Pelekanos R.A. Gardon O. Tunny K.A. Blucher K.M. Morton C.J. Parker M.W. Sierecki E. Gambin Y. Gomez G.A. Alexandrov K. et al.Mechanism of activation of protein kinase JAK2 by the growth hormone receptor.Science. 2014; 344: 1249783Crossref PubMed Scopus (231) Google Scholar, 30Varghese L.N. Ungureanu D. Liau N.P.D. Young S.N. Laktyushin A. Hammarén H. Lucet I.S. Nicola N.A. Silvennoinen O. Babon J.J. Murphy J.M. Mechanistic insights into activation and SOCS3-mediated inhibition of myeloproliferative neoplasm-associated JAK2 mutants from biochemical and structural analyses.Biochem. J. 2014; 458: 395-405Crossref PubMed Scopus (0) Google Scholar, 31Babon J.J. Lucet I.S. Murphy J.M. Nicola N.A. Varghese L.N. The molecular regulation of Janus kinase (JAK) activation.Biochem. J. 2014; 462: 1-13Crossref PubMed Scopus (143) Google Scholar). While the mechanism is still debated (31Babon J.J. Lucet I.S. Murphy J.M. Nicola N.A. Varghese L.N. The molecular regulation of Janus kinase (JAK) activation.Biochem. J. 2014; 462: 1-13Crossref PubMed Scopus (143) Google Scholar), this function was clearly revealed by the discovery of activating pseudokinase domain mutations (32James C. Ugo V. Le Couédic J.-P. Staerk J. Delhommeau F. Lacout C. Garçon L. Raslova H. Berger R. Bennaceur-Griscelli A. Villeval J.L. Constantinescu S.N. Casadevall N. Vainchenker W. A unique clonal JAK2 mutation leading to constitutive signalling causes polycythaemia vera.Nature. 2005; 434: 1144-1148Crossref PubMed Scopus (2692) Google Scholar), which promote JAK2 signaling and induce hematopoietic malignancies. Accordingly, from duplications of their kinase ancestors, pseudokinases can evolve pseudoactive sites that do not bind nucleotide, diminish their activation loops, and adopt conformations discordant with catalytic activity. Any of these modifications enable function as protein interaction domains that regulate activities of their cognate kinase partners allosterically. Via intermolecular interactions, kinases and pseudokinases are able to modulate the position of the key regulatory element, the αC helix within the N-lobe of the kinase fold, to promote active or inactive conformations of the catalytically active partner kinase. Several distinct modes of dimerization have been reported to influence the position of αC helix, which have been illuminated by detailed structural studies, and highlight the versatility of the kinase fold as a protein interaction domain (Fig. 3; (33Lavoie H. Li J.J. Thevakumaran N. Therrien M. Sicheri F. Dimerization-induced allostery in protein kinase regulation.Trends Biochem. Sci. 2014; 39: 475-486Abstract Full Text Full Text PDF PubMed Google Scholar, 34Oliver M.R. Horne C.R. Shrestha S. Keown J.R. Liang L.-Y. Young S.N. Sandow J.J. Webb A.I. Goldstone D.C. Lucet I.S. Kannan N. Metcalf P. Murphy J.M. Granulovirus PK-1 kinase activity relies on a side-to-side dimerization mode centered on the regulatory αC helix.Nat. Commun. 2021; 12: 1002Crossref PubMed Scopus (1) Google Scholar, 35Horne C.R. Murphy J.M. For whom the bell tolls: The structure of the dead kinase, IRAK3.Structure. 2021; 29: 197-199Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar)). Many of the different regulatory binding modes are illustrated by pseudokinase domain binding to a cognate kinase or pseudokinase domain, including: back-to-back (as observed for Ire1 and RNase L homodimers (36Lee K.P.K. Dey M. Neculai D. Cao C. Dever T.E. Sicheri F. Structure of the dual enzyme Ire1 reveals the basis for catalysis and regulation in nonconventional RNA splicing.Cell. 2008; 132: 89-100Abstract Full Text Full Text PDF PubMed Scopus (238) Google Scholar, 37Huang H. Zeqiraj E. Dong B. Jha B.K. Duffy N.M. Orlicky S. Thevakumaran N. Talukdar M. Pillon M.C. Ceccarelli D.F. Wan L.C.K. Juang Y.-C. Mao D.Y.L. Gaughan C. Brinton M.A. et al.Dimeric structure of pseudokinase RNase L bound to 2-5A reveals a basis for interferon-induced antiviral activity.Mol. Cell. 2014; 53: 221-234Abstract Full Text Full Text PDF PubMed Scopus (83) Google Scholar), head-to-tail (as observed for EGFR family proteins, such as HER3 pseudokinase:EGFR kinase (38Littlefield P. Liu L. Mysore V. Shan Y. Shaw D.E. Jura N. Structural analysis of the EGFR/HER3 heterodimer reveals the molecular basis for activating HER3 mutations.Sci. Signal. 2014; 7ra114Crossref PubMed Google Scholar)), head-to-head (as found for IRAK3 homodimers and proposed for IRAK3 pseudokinase:IRAK4 kinase pairs (39Lange S.M. Nelen M.I. Cohen P. Kulathu Y. Dimeric structure of the pseudokinase IRAK3 suggests an allosteric mechanism for negative regulation.Structure. 2021; 29: 238-251.e4Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar)), and antiparallel side-to-side (exemplified for RAF:RAF kinase dimers and KSR pseudokinase:RAF kinase heterodimers (40Hu J. Stites E.C. Yu H. Germino E.A. Meharena H.S. Stork P.J.S. Kornev A.P. Taylor S.S. Shaw A.S. Allosteric activation of functionally asymmetric RAF kinase dimers.Cell. 2013; 154: 1036-1046Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar, 41Hatzivassiliou G. Song K. Yen I. Brandhuber B.J. Anderson D.J. Alvarado R. Ludlam M.J.C. Stokoe D. Gloor S.L. Vigers G. Morales T. Aliagas I. Liu B. Sideris S. Hoeflich K.P. et al.RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth.Nature. 2010; 464: 431-435Crossref PubMed Scopus (1177) Google Scholar, 42Rajakulendran T. Sahmi M. Lefrançois M. Sicheri F. Therrien M. A dimerization-dependent mechanism drives RAF catalytic activation.Nature. 2009; 461: 542-545Crossref PubMed Scopus (0) Google Scholar)) modes. These studies raise the possibility that protein kinases may exert noncatalytic regulatory roles on other kinases, similar to those exerted by pseudokinases, as recently proposed for the parallel side-to-side mode of homodimerization reported for the granuloviral PK-1 kinase (34Oliver M.R. Horne C.R. Shrestha S. Keown J.R. Liang L.-Y. Young S.N. Sandow J.J. Webb A.I. Goldstone D.C. Lucet I.S. Kannan N. Metcalf P. Murphy J.M. Granulovirus PK-1 kinase activity relies on a side-to-side dimerization mode centered on the regulatory αC helix.Nat. Commun. 2021; 12: 1002Crossref PubMed Scopus (1) Google Scholar). While not yet observed among pseudokinase:kinase pairs, this binding mode couples dimerization with the αC helix occupying a position synonymous with catalytic activity. Furthermore, while currently poorly understood, some pseudokinases have been reported to allosterically regulate the activities of nonkinase enzymes, as proposed for VRK3 pseudokinase binding to, and activation of, the VHR phosphatase (43Scheeff E.D. Eswaran J. Bunkóczi G. Knapp S. Manning G. Structure of the pseudokinase VRK3 reveals a degraded catalytic site, a highly conserved kinase fold, and a putative regulatory binding site.Structure. 2009; 17: 128-138Abstract Full Text Full Text PDF PubMed Scopus (127) Google Scholar, 44Kang T.-H. Kim K.-T. Negative regulation of ERK activity by VRK3-mediated activation of VHR phosphatase.Nat. Cell Biol. 2006; 8: 863-869Crossref PubMed Scopus (64) Google Scholar). Overall, these findings illustrate the breadth of noncatalytic allosteric functions that can be mediated by pseudokinase domains and suggest these may be underappreciated functions of protein kinases more generally. Deducing the precise nature of these noncatalytic allosteric functions of conventional protein kinases remains a major challenge. Such studies will rely on elegant chemical biology and catalytically dead knockin approaches, rather than gene deletion or knockdown, to reveal functions beyond phosphoryl transfer. Over the past 30 years, crystal structures of kinase and pseudokinase domains have captured the N- and C-lobes and the regulatory elements, the αC helix and activation loop, and structural pillars of hydrophobic networks (termed spines) in a continuum of conformations, illustrating their intrinsic dynamicity (45Kornev A.P. Taylor S.S. Dynamics-driven allostery in protein kinases.Trends Biochem. Sci. 2015; 40: 628-647Abstract Full Text Full Text PDF PubMed Scopus (136) Google Scholar, 46Taylor S.S. Kornev A.P. Protein kinases: Evolution of dynamic regulatory proteins.Trends Biochem. Sci. 2011; 36: 65-77Abstract Full Text Full Text PDF PubMed Scopus (517) Google Scholar, 47Modi V. Dunbrack Jr., R.L. Defining a new nomenclature for the structures of active and inactive kinases.Proc. Natl. Acad. Sci. U. S. A. 2019; 116: 6818-6827Crossref PubMed Scopus (47) Google Scholar). In the case of conventional, active kinases, this flexibility has been associated with regulation of catalytic activity. Basally, the apoenzyme is proposed to exist in a catalytically uncommitted state until ATP binding, which galvanizes the protein's internal hydrophobic networks and poises the kinase for catalysis. Allosteric effectors and oligomerization are known to modulate adoption of a catalytically active conformation signified by an intact regulatory (R)-spine and αC helix Glu engaged in a salt bridge with the β3-strand Lys (45Kornev A.P. Taylor S.S. Dynamics-driven allostery in protein kinases.Trends Biochem. Sci. 2015; 40: 628-647Abstract Full Text Full Text PDF PubMed Scopus (136) Google Scholar). However, what if, more broadly, the range of conformations accessible by kinase and pseudokinase domains might reflect their propensity to serve as molecular switches? Recent studies have revealed that beyond the catalytic functions of kinases, both they and pseudokinases serve important signaling functions via protein–protein interactions. Consequently, an attractive hypothesis is that the propensity for these interactions could be governed by the conformation of the kinase or pseudokinase, and additionally, these conformations might be regulated by binding partners or posttranslational modifications. The concept of the kinase fold being employed by nature as a molecular switch is best illustrated by the Mixed Lineage Kinase domain-Like (MLKL) pseudokinase. Unlike conventional kinases, it functions solely as a protein interaction domain, and thus interpretation of conformational effects is not confounded by an additional catalytic activity function exerted by active kinases. MLKL is the terminal effector in the necroptosis cell death pathway, which is a lytic cell death modality that, unlike the cousin pathway apoptosis, does not rely on the proteolytic functions of Caspases (reviewed in (48Samson A.L. Garnish S.E. Hildebrand J.M. Murphy J.M. Location, location, location: A compartmentalized view of TNF-induced necroptotic signaling.Sci. Signal. 2021; 14eabc6178Crossref PubMed Scopus (3) Google Scholar)). Instead, necroptosis arises following an insult, such as inflammatory death receptor signaling or activation of innate pathogen sensors, which leads to oligomerization and activation of the receptor-interacting protein kinase-3 (RIPK3) effector kinase by autophosphorylation (reviewed in (49Meng Y. Sandow J.J. Czabotar P.E. Murphy J.M. The regulation of necroptosis by post-translational modifications.Cell Death Differ. 2021; 28: 861-883Crossref PubMed Scopus (2) Google Scholar)). Activated RIPK3 can then phosphorylate its substrate, MLKL, on the ac
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