CoChat
Sign Up
Cited by 5Protein Kinase Regulation and GTPase SignalingHeat shock proteins researchProtein Structure and Dynamics

The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.

Evolutionary and cellular analysis of the ‘dark’ pseudokinase PSKH2

Open access
Byrne, Dominic P., Shrestha, Safal, Daly, Leonard A., Marensi, Vanessa, Ramakrishnan, Krithika, Eyers, Claire E., Kannan, Natarajan, Eyers, Patrick A.·2023·Biochemical Journal
DOI 10.1042/bcj20220474PMC PMC9988210

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

Pseudokinases, so named because they lack one or more conserved canonical amino acids that define their catalytically active relatives, have evolved a variety of biological functions in both prokaryotic and eukaryotic organisms. Human PSKH2 is closely related to the canonical kinase PSKH1, which maps to the CAMK family of protein kinases. Primates encode PSKH2 in the form of a pseudokinase, which is predicted to be catalytically inactive due to loss of the invariant catalytic Asp residue. Although the biological role(s) of vertebrate PSKH2 proteins remains unclear, we previously identified species-level adaptions in PSKH2 that have led to the appearance of kinase or pseudokinase variants in vertebrate genomes alongside a canonical PSKH1 paralog. In this paper we confirm that, as predicted, PSKH2 lacks detectable protein phosphotransferase activity, and exploit structural informatics, biochemistry and cellular proteomics to begin to characterise vertebrate PSKH2 orthologues. AlphaFold 2-based structural analysis predicts functional roles for both the PSKH2 N- and C-regions that flank the pseudokinase domain core, and cellular truncation analysis confirms that the N-terminal domain, which contains a conserved myristoylation site, is required for both stable human PSKH2 expression and localisation to a membrane-rich subcellular fraction containing mitochondrial proteins. Using mass spectrometry-based proteomics, we confirm that human PSKH2 is part of a cellular mitochondrial protein network, and that its expression is regulated through client-status within the HSP90/Cdc37 molecular chaperone system. HSP90 interactions are mediated through binding to the PSKH2 C-terminal tail, leading us to predict that this region might act as both a cis and trans regulatory element, driving outputs linked to the PSKH2 pseudokinase domain that are important for functional signalling.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1042/bcj20220474

Cites

7 of 7 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 74

  1. 2017, Live and let die: insights into pseudoenzyme mechanisms from structure, Curr. Opin. Struct. Biol., 47, 95, 10.1016/j.sbi.2017.07.004 · DOI
  2. 2002, The protein kinase complement of the human genome, Science, 298, 1912, 10.1126/science.1075762 · DOI · Paper page
  3. 2006, Emerging roles of pseudokinases, Trends Cell Biol., 16, 443, 10.1016/j.tcb.2006.07.003 · DOI
  4. 2020, Cataloguing the dead: breathing new life into pseudokinase research, FEBS J., 287, 4150, 10.1111/febs.15246 · DOI
  5. 2010, The (un) targeted cancer kinome, Nat. Chem. Biol., 6, 166, 10.1038/nchembio.297 · DOI
  6. 2021, There's more to death than life: Noncatalytic functions in kinase and pseudokinase signaling, J. Biol. Chem., 296, 100705, 10.1016/j.jbc.2021.100705 · DOI
  7. 2021, The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases, Nucleic Acids Res., 49, D529, 10.1093/nar/gkaa853 · DOI
  8. 2000, Characterization of PSKH1, a novel human protein serine kinase with centrosomal, Golgi, and nuclear localization, Genomics, 70, 82, 10.1006/geno.2000.6365 · DOI
  9. 1995, The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification 1, FASEB J., 9, 576, 10.1096/fasebj.9.8.7768349 · DOI
  10. 2007, The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module, Proc. Natl Acad. Sci. U.S.A., 104, 1272, 10.1073/pnas.0610251104 · DOI
  11. 2018, Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells, Sci. Signal., 11, eaat7951, 10.1126/scisignal.aat7951 · DOI
  12. 2011, The pseudokinase domain of JAK2 is a dual-specificity protein kinase that negatively regulates cytokine signaling, Nat. Struct. Mol. Biol., 18, 971, 10.1038/nsmb.2099 · DOI
  13. 2010, Erbb3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation, Proc. Natl Acad. Sci. U.S.A., 107, 7692, 10.1073/pnas.1002753107 · DOI
  14. 2003, Mutants of the protein serine kinase PSKH1 disassemble the Golgi apparatus, Exp. Cell Res., 291, 299, 10.1016/j.yexcr.2003.07.009 · DOI
  15. 2020, The clinical kinase index: a method to prioritize understudied kinases as drug targets for the treatment of cancer, Cell Rep. Med., 1, 100128, 10.1016/j.xcrm.2020.100128 · DOI
  16. 2013, Cancer genome landscapes, Science, 339, 1546, 10.1126/science.1235122 · DOI · Paper page
  17. 2008, Kinase requirements in human cells: I. comparing kinase requirements across various cell types, Proc. Natl Acad. Sci. U.S.A., 105, 16472, 10.1073/pnas.0808019105 · DOI
  18. 2015, A comprehensive transcriptional portrait of human cancer cell lines, Nat. Biotechnol., 33, 306, 10.1038/nbt.3080 · DOI
  19. 2009, A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene, Cell, 137, 835, 10.1016/j.cell.2009.05.006 · DOI · Paper page
  20. 2022, Dark kinase annotation, mining and visualization using the Protein Kinase Ontology, bioRxiv, 10.1101/2022.02.25.482021 · DOI
  21. 2022, Computational tools and resources for pseudokinase research, Methods Enzymol., 667, 403, 10.1016/bs.mie.2022.03.040 · DOI
  22. 2019, Tracing the origin and evolution of pseudokinases across the tree of life, Sci. Signal., 12, eaav3810, 10.1126/scisignal.aav3810 · DOI
  23. 2021, Kinortho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases, BMC Bioinformatics, 22, 446, 10.1186/s12859-021-04358-3 · DOI
  24. 2017, Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree, bioRxiv, 10.1101/181966 · DOI
  25. 2020, N-myristoylation: from cell biology to translational medicine, Acta Pharmacol. Sin., 41, 1005, 10.1038/s41401-020-0388-4 · DOI
  26. 2008, CASK functions as a Mg2+-independent neurexin kinase, Cell, 133, 328, 10.1016/j.cell.2008.02.036 · DOI · Paper page
  27. 2015, The Tribbles 2 (TRB2) pseudokinase binds to ATP and autophosphorylates in a metal-independent manner, Biochem. J., 467, 47, 10.1042/bj20141441 · DOI
  28. 2012, Uncoordinated (UNC)119: coordinating the trafficking of myristoylated proteins, Vis. Res., 75, 26, 10.1016/j.visres.2012.08.012 · DOI
  29. 2021, Dual proteome-scale networks reveal cell-specific remodeling of the human interactome, Cell, 184, 3022, 10.1016/j.cell.2021.04.011 · DOI · Paper page
  30. 2019, Metascape provides a biologist-oriented resource for the analysis of systems-level datasets, Nat. Commun., 10, 1523, 10.1038/s41467-019-09234-6 · DOI · Paper page
  31. 2015, Proteomics. Tissue-based map of the human proteome, Science, 347, 1260419, 10.1126/science.1260419 · DOI · Paper page
  32. 2021, A subcellular map of the human kinome, eLife, 10, e64943, 10.7554/eLife.64943 · DOI
  33. Calderwood, 2007, Cell Stress Proteins, 326, 10.1007/978-0-387-39717-7 · DOI
  34. 2019, Therapeutic potential of the Hsp90/Cdc37 interaction in neurodegenerative diseases, Front. Neurosci., 13, 1263, 10.3389/fnins.2019.01263 · DOI
  35. 2020, Kinase interaction network expands functional and disease roles of human kinases, Mol. Cell, 79, 504, 10.1016/j.molcel.2020.07.001 · DOI
  36. 2000, The heat shock protein 90 antagonist geldanamycin alters chaperone association with p210bcr-abl and v-src proteins before their degradation by the proteasome, Cell Growth Differ., 11, 355
  37. 2001, Geldanamycin and its analogue 17-allylamino-17-demethoxygeldanamycin lowers Bcr-Abl levels and induces apoptosis and differentiation of Bcr-Abl-positive human leukemic blasts, Cancer Res., 61, 1799
  38. 1997, Geldanamycin-induced destabilization of Raf-1 involves the proteasome, Biochem. Biophys. Res. Commun., 239, 655, 10.1006/bbrc.1997.7527 · DOI
  39. 2008, A novel Hsp90 inhibitor to disrupt Hsp90/Cdc37 complex against pancreatic cancer cells, Mol. Cancer Ther., 7, 162, 10.1158/1535-7163.Mct-07-0484 · DOI
  40. 2010, Microarray analysis of the effect of dexamethasone on murine cochlear explants, Acta Otolaryngol., 130, 1329, 10.3109/00016489.2010.498836 · DOI
  41. 2012, Intratympanic dexamethasone up-regulates Fkbp5 in the cochleae of mice in vivo, Acta Otolaryngol., 132, 4, 10.3109/00016489.2011.619571 · DOI
  42. 2005, Phase I pharmacokinetic and pharmacodynamic study of 17-allylamino, 17-demethoxygeldanamycin in patients with advanced malignancies, J. Clin. Oncol., 23, 4152, 10.1200/JCO.2005.00.612 · DOI
  43. 2009, Targeted therapy of human osteosarcoma with 17AAG or rapamycin: characterization of induced apoptosis and inhibition of mTOR and Akt/MAPK/Wnt pathways, Int. J. Oncol., 34, 551, 10.3892/ijo_00000181 · DOI
  44. 2009, Importing mitochondrial proteins: machineries and mechanisms, Cell, 138, 628, 10.1016/j.cell.2009.08.005 · DOI
  45. 2021, Targeting PINK1 using natural products for the treatment of human diseases, Biomed. Res. Int., 2021, 4045819, 10.1155/2021/4045819 · DOI
  46. 2018, Identification and characterization of protein N-myristoylation occurring on four human mitochondrial proteins, SAMM50, TOMM40, MIC19, and MIC25, PLoS ONE, 13, e0206355, 10.1371/journal.pone.0206355 · DOI
  47. 2015, Myristoylation confers noncanonical AMPK functions in autophagy selectivity and mitochondrial surveillance, Nat. Comm., 6, 7926, 10.1038/ncomms8926 · DOI
  48. 2018, Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus, Nat. Chem., 10, 599, 10.1038/s41557-018-0039-2 · DOI
  49. 2017, Pseudokinases: update on their functions and evaluation as new drug targets, Future Med. Chem., 9, 245, 10.4155/fmc-2016-0207 · DOI
  50. 2014, A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties, Biochem. J., 457, 323, 10.1042/BJ20131174 · DOI
  51. 2019, Prospects for pharmacological targeting of pseudokinases, Nat. Rev. Drug Discov., 18, 501, 10.1038/s41573-019-0018-3 · DOI
  52. 2019, Hsp90 and Hsp70 chaperones: Collaborators in protein remodeling, J. Biol. Chem., 294, 2109, 10.1074/jbc.REV118.002806 · DOI
  53. 2018, Dancing with the diva: Hsp90–client interactions, J. Mol. Biol., 430, 3029, 10.1016/j.jmb.2018.05.026 · DOI
  54. 1982, n-Tetradecanoyl is the NH2-terminal blocking group of the catalytic subunit of cyclic AMP-dependent protein kinase from bovine cardiac muscle, Proc. Natl Acad. Sci. U.S.A., 79, 6128, 10.1073/pnas.79.20.6128 · DOI
  55. 2003, A myristoyl/phosphotyrosine switch regulates c-Abl, Cell, 112, 845, 10.1016/s0092-8674(03)00191-0 · DOI
  56. 2021, Protein N-myristoylation: functions and mechanisms in control of innate immunity, Cell. Mol. Immunol., 18, 878, 10.1038/s41423-021-00663-2 · DOI
  57. 2019, Myristoylation-dependent palmitoylation of the receptor tyrosine kinase adaptor FRS2α, Biochemistry, 58, 2809, 10.1021/acs.biochem.9b00299 · DOI
  58. 1994, N-terminally myristoylated Ras proteins require palmitoylation or a polybasic domain for plasma membrane localization, Mol. Cell. Biol., 14, 4722, 10.1128/mcb.14.7.4722-4730.1994 · DOI
  59. 2013, Direct detection of S-palmitoylation by mass spectrometry, Anal. Chem., 85, 11952, 10.1021/ac402850s · DOI
  60. 2016, Protein prenylation: unique fats make their mark on biology, Nat. Rev. Mol. Cell Biol., 17, 110, 10.1038/nrm.2015.11 · DOI
  61. 2020, Myristoylation, an ancient protein modification mirroring eukaryogenesis and evolution, Trends Biochem. Sci., 45, 619, 10.1016/j.tibs.2020.03.007 · DOI
  62. 2021, Myristoylation alone is sufficient for PKA catalytic subunits to associate with the plasma membrane to regulate neuronal functions, Proc. Natl Acad. Sci. U.S.A., 118, e2021658118, 10.1073/pnas.2021658118 · DOI
  63. 2018, Aurora kinase A localises to mitochondria to control organelle dynamics and energy production, eLife, 7, e38111, 10.7554/eLife.38111 · DOI
  64. 2013, Dawn of the dead: protein pseudokinases signal new adventures in cell biology, Biochem. Soc. Trans., 41, 969, 10.1042/BST20130115 · DOI
  65. 2014, Day of the dead: pseudokinases and pseudophosphatases in physiology and disease, Trends Cell Biol., 24, 489, 10.1016/j.tcb.2014.03.008 · DOI
  66. 2017, Evaluation of parameters for confident phosphorylation site localization using an orbitrap fusion tribrid mass spectrometer, J. Proteome Res., 16, 3448, 10.1021/acs.jproteome.7b00337 · DOI
  67. 2021, Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1α/2α, Sci. Signal., 14, eabf6685, 10.1126/scisignal.abf6685 · DOI
  68. 2005, GROMACS: fast, flexible, and free, J. Comput. Chem., 26, 1701, 10.1002/jcc.20291 · DOI
  69. 2004, Development and testing of a general amber force field, J. Comput. Chem., 25, 1157, 10.1002/jcc.20035 · DOI
  70. 2010, Molecular dynamics simulation with weak coupling to heat and material baths, J. Chem. Phys., 133, 084105, 10.1063/1.3474951 · DOI
  71. 2013, A flexible algorithm for calculating pair interactions on SIMD architectures, Comput. Phys. Commun., 184, 2641, 10.1016/j.cpc.2013.06.003 · DOI
  72. 2007, Canonical sampling through velocity rescaling, J. Chem. Phys., 126, 014101, 10.1063/1.2408420 · DOI
  73. 2021, Protein complex prediction with AlphaFold-Multimer, bioRxiv, 10.1101/2021.10.04.463034 · DOI · Paper page
  74. 2004, Weblogo: a sequence logo generator, Genome Res., 14, 1188, 10.1101/gr.849004 · DOI

Metadata

Authors
Byrne, D. P., Shrestha, S., Daly, L. A., Marensi, V., Ramakrishnan, K., Eyers, C. E., Kannan, N., & Eyers, P. A.
Affiliations
  • University of Liverpool (GB)
  • University of Georgia (US)
Corresponding author
Kannan, Natarajan
ORCID
Venue
Biochemical Journal
Publisher
Portland Press Ltd.
Published
2023-01-23
Volume
480
Issue
2
Pages
141-160
ISSN
  • 0264-6021 (ISSN-L)
  • 1470-8728
DOI
10.1042/bcj20220474
PMC
PMC9988210
OpenAlex
W4311547358
Cited by
5
References
7
Citations by year
2026: 1 · 2025: 2 · 2024: 1 · 2023: 1
FWCI
0.33
Type
journal article
Language
en
Open access
Licence
Locations
  • Biochemical Journal (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • North West Cancer Research (CR1208, CR1097)
  • National Institutes of Health (BB/N021703/1, BB/S018514/1)
  • Biotechnology and Biological Sciences Research Council (BB/N021703/1, BB/S018514/1, BB/N021703, BB/R000182/1)
  • National Cancer Institute (U01CA239106)
  • Common Fund (U01CA239106)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Heat shock proteins research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
pseudokinase, protein kinase evolution, myristoylation, subcellular localization
MeSH terms
Animals, Biological Evolution, Humans, Phosphorylation, Protein Kinases, Signal Transduction, Molecular Chaperones, HSP90 Heat-Shock Proteins

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review