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      Emerging functions of pseudoenzymes

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          Abstract

          As sequence and structural databases grow along with powerful analysis tools, the prevalence and diversity of pseudoenzymes have become increasingly evident. Pseudoenzymes are present across the tree of life in a large number of enzyme families. Pseudoenzymes are defined as proteins that lack conserved catalytic motifs based on sequence analysis. However, some pseudoenzymes may have migrated amino acids necessary for catalysis, allowing them to catalyze enzymatic reactions. Furthermore, pseudoenzymes retain several non-enzymatic functions such as allosteric regulation, signal integration, scaffolding, and competitive inhibition. In this review, we provide examples of each mode of action using the pseudokinase, pseudophosphatase, and pseudo ADP-ribosyltransferase families. We highlight the methodologies that facilitate the biochemical and functional characterization of pseudoenzymes to encourage further investigation in this burgeoning field.

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          Most cited references136

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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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            Mixed lineage kinase domain-like protein MLKL causes necrotic membrane disruption upon phosphorylation by RIP3.

            Programmed necrotic cell death induced by the tumor necrosis factor alpha (TNF-α) family of cytokines is dependent on a kinase cascade consisting of receptor-interacting kinases RIP1 and RIP3. How these kinase activities cause cells to die by necrosis is not known. The mixed lineage kinase domain-like protein MLKL is a functional RIP3 substrate that binds to RIP3 through its kinase-like domain but lacks kinase activity of its own. RIP3 phosphorylates MLKL at the T357 and S358 sites. Reported here is the development of a monoclonal antibody that specifically recognizes phosphorylated MLKL in cells dying of this pathway and in human liver biopsy samples from patients suffering from drug-induced liver injury. The phosphorylated MLKL forms an oligomer that binds to phosphatidylinositol lipids and cardiolipin. This property allows MLKL to move from the cytosol to the plasma and intracellular membranes, where it directly disrupts membrane integrity, resulting in necrotic death. Copyright © 2014 Elsevier Inc. All rights reserved.
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              Evolution of protein kinase signaling from yeast to man.

              Protein phosphorylation controls many cellular processes, especially those involved in intercellular communication and coordination of complex functions. To explore the evolution of protein phosphorylation, we compared the protein kinase complements ('kinomes') of budding yeast, worm and fly, with known human kinases. We classify kinases into putative orthologous groups with conserved functions and discuss kinase families and pathways that are unique, expanded or lost in each lineage. Fly and human share several kinase families involved in immunity, neurobiology, cell cycle and morphogenesis that are absent from worm, suggesting that these functions might have evolved after the divergence of nematodes from the main metazoan lineage.
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                Author and article information

                Journal
                Biochem J
                Biochem J
                BCJ
                Biochemical Journal
                Portland Press Ltd.
                0264-6021
                1470-8728
                31 May 2023
                19 May 2023
                : 480
                : 10
                : 715-728
                Affiliations
                [1 ]Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, U.S.A.
                [2 ]Center for Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, TX, U.S.A.
                Author notes
                Correspondence: Anju Sreelatha ( anju.sreelatha@ 123456utsouthwestern.edu )
                Author information
                http://orcid.org/0000-0001-9485-0214
                Article
                BCJ-480-715
                10.1042/BCJ20220373
                10211241
                37204401
                599f8aea-8934-4d94-bb23-e7dd23fbdc2a
                © 2023 The Author(s)

                This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY). Open access for this article was enabled by the participation of the University of Texas Southwestern Medical Center in an all-inclusive Read & Publish agreement with Portland Press and the Biochemical Society under a transformative agreement with Individual.

                History
                : 17 December 2022
                : 27 April 2023
                : 28 April 2023
                Categories
                Enzymology
                Structural Biology
                Post-Translational Modifications
                Molecular Interactions
                Review Articles

                Biochemistry
                allosteric regulation,catalytic motif,molecular scaffolds,molecular switch,protein moonlighting,substrate trap

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