Regulation of RAS palmitoyltransferases by accessory proteins and palmitoylation.
Journal
Nature structural & molecular biology
ISSN: 1545-9985
Titre abrégé: Nat Struct Mol Biol
Pays: United States
ID NLM: 101186374
Informations de publication
Date de publication:
Mar 2024
Mar 2024
Historique:
received:
02
03
2023
accepted:
17
11
2023
pubmed:
6
1
2024
medline:
6
1
2024
entrez:
5
1
2024
Statut:
ppublish
Résumé
Palmitoylation of cysteine residues at the C-terminal hypervariable regions in human HRAS and NRAS, which is necessary for RAS signaling, is catalyzed by the acyltransferase DHHC9 in complex with its accessory protein GCP16. The molecular basis for the acyltransferase activity and the regulation of DHHC9 by GCP16 is not clear. Here we report the cryo-electron microscopy structures of the human DHHC9-GCP16 complex and its yeast counterpart-the Erf2-Erf4 complex, demonstrating that GCP16 and Erf4 are not directly involved in the catalytic process but stabilize the architecture of DHHC9 and Erf2, respectively. We found that a phospholipid binding to an arginine-rich region of DHHC9 and palmitoylation on three residues (C24, C25 and C288) were essential for the catalytic activity of the DHHC9-GCP16 complex. Moreover, we showed that GCP16 also formed complexes with DHHC14 and DHHC18 to catalyze RAS palmitoylation. These findings provide insights into the regulatory mechanism of RAS palmitoyltransferases.
Identifiants
pubmed: 38182928
doi: 10.1038/s41594-023-01183-5
pii: 10.1038/s41594-023-01183-5
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
436-446Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Simanshu, D. K., Nissley, D. V. & McCormick, F. RAS proteins and their regulators in human disease. Cell 170, 17–33 (2017).
doi: 10.1016/j.cell.2017.06.009
pubmed: 28666118
pmcid: 5555610
Hancock, J. F., Magee, A. I., Childs, J. E. & Marshall, C. J. All ras proteins are polyisoprenylated but only some are palmitoylated. Cell 57, 1167–1177 (1989).
doi: 10.1016/0092-8674(89)90054-8
pubmed: 2661017
Campbell, S. L. & Philips, M. R. Post-translational modification of RAS proteins. Curr. Opin. Struct. Biol. 71, 180–192 (2021).
doi: 10.1016/j.sbi.2021.06.015
pubmed: 34365229
pmcid: 8649064
Rocks, O. et al. An acylation cycle regulates localization and activity of palmitoylated Ras isoforms. Science 307, 1746–1752 (2005).
doi: 10.1126/science.1105654
pubmed: 15705808
Zambetti, N. A. et al. Genetic disruption of N-RasG12D palmitoylation perturbs hematopoiesis and prevents myeloid transformation in mice. Blood 135, 1772–1782 (2020).
doi: 10.1182/blood.2019003530
pubmed: 32219446
pmcid: 7225687
Remsberg, J. R. et al. ABHD17 regulation of plasma membrane palmitoylation and N-Ras-dependent cancer growth. Nat. Chem. Biol. 17, 856–864 (2021).
doi: 10.1038/s41589-021-00785-8
pubmed: 33927411
pmcid: 8900659
Swarthout, J. T. et al. DHHC9 and GCP16 constitute a human protein fatty acyltransferase with specificity for H- and N-Ras. J. Biol. Chem. 280, 31141–31148 (2005).
doi: 10.1074/jbc.M504113200
pubmed: 16000296
Jiang, H. et al. Protein lipidation: occurrence, mechanisms, biological functions, and enabling technologies. Chem. Rev. 118, 919–988 (2018).
doi: 10.1021/acs.chemrev.6b00750
pubmed: 29292991
pmcid: 5985209
Rana, M. S. et al. Fatty acyl recognition and transfer by an integral membrane S-acyltransferase. Science 359, eaao6326 (2018).
doi: 10.1126/science.aao6326
pubmed: 29326245
pmcid: 6317078
Lee, C. J. et al. Bivalent recognition of fatty acyl-CoA by a human integral membrane palmitoyltransferase. Proc. Natl Acad. Sci. USA 119, e2022050119 (2022).
doi: 10.1073/pnas.2022050119
pubmed: 35140179
pmcid: 8851515
Lobo, S., Greentree, W. K., Linder, M. E. & Deschenes, R. J. Identification of a Ras palmitoyltransferase in Saccharomyces cerevisiae. J. Biol. Chem. 277, 41268–41273 (2002).
doi: 10.1074/jbc.M206573200
pubmed: 12193598
Bartels, D. J., Mitchell, D. A., Dong, X. & Deschenes, R. J. Erf2, a novel gene product that affects the localization and palmitoylation of Ras2 in Saccharomyces cerevisiae. Mol. Cell. Biol. 19, 6775–6787 (1999).
doi: 10.1128/MCB.19.10.6775
pubmed: 10490616
pmcid: 84674
Mitchell, D. A. et al. The Erf4 subunit of the yeast Ras palmitoyl acyltransferase is required for stability of the Acyl–Erf2 intermediate and palmitoyl transfer to a Ras2 substrate. J. Biol. Chem. 287, 34337–34348 (2012).
doi: 10.1074/jbc.M112.379297
pubmed: 22904317
pmcid: 3464540
Verardi, R., Kim, J. S., Ghirlando, R. & Banerjee, A. Structural basis for substrate recognition by the ankyrin repeat domain of human DHHC17 palmitoyltransferase. Structure 25, 1337–1347 e1336 (2017).
doi: 10.1016/j.str.2017.06.018
pubmed: 28757145
pmcid: 5599134
Kuroda, Y., Suzuki, N. & Kataoka, T. The effect of posttranslational modifications on the interaction of Ras2 with adenylyl cyclase. Science 259, 683–686 (1993).
doi: 10.1126/science.8430318
pubmed: 8430318
Mitchell, D. A. et al. Mutations in the X-linked intellectual disability gene, zDHHC9, alter autopalmitoylation activity by distinct mechanisms. J. Biol. Chem. 289, 18582–18592 (2014).
doi: 10.1074/jbc.M114.567420
pubmed: 24811172
pmcid: 4140262
Apolloni, A., Prior, I. A., Lindsay, M., Parton, R. G. & Hancock, J. F. H-ras but not K-ras traffics to the plasma membrane through the exocytic pathway. Mol. Cell. Biol. 20, 2475–2487 (2000).
doi: 10.1128/MCB.20.7.2475-2487.2000
pubmed: 10713171
pmcid: 85443
Ahearn, I. M. et al. FKBP12 binds to acylated H-ras and promotes depalmitoylation. Mol. Cell 41, 173–185 (2011).
doi: 10.1016/j.molcel.2011.01.001
pubmed: 21255728
pmcid: 3085165
Chai, S., Cambronne, X. A., Eichhorn, S. W. & Goodman, R. H. MicroRNA-134 activity in somatostatin interneurons regulates H-Ras localization by repressing the palmitoylation enzyme, DHHC9. Proc. Natl Acad. Sci. USA 110, 17898–17903 (2013).
doi: 10.1073/pnas.1317528110
pubmed: 24127608
pmcid: 3816481
Dong, X. et al. Palmitoylation and plasma membrane localization of Ras2p by a nonclassical trafficking pathway in Saccharomyces cerevisiae. Mol. Cell. Biol. 23, 6574–6584 (2003).
doi: 10.1128/MCB.23.18.6574-6584.2003
pubmed: 12944483
pmcid: 193718
Nishio, M., Umezawa, Y., Fantini, J., Weiss, M. S. & Chakrabarti, P. CH–π hydrogen bonds in biological macromolecules. Phys. Chem. Chem. Phys. 16, 12648–12683 (2014).
doi: 10.1039/C4CP00099D
pubmed: 24836323
Ohta, E. et al. Identification and characterization of GCP16, a novel acylated Golgi protein that interacts with GCP170. J. Biol. Chem. 278, 51957–51967 (2003).
doi: 10.1074/jbc.M310014200
pubmed: 14522980
Ko, P. J. et al. A ZDHHC5–GOLGA7 protein acyltransferase complex promotes nonapoptotic cell death. Cell Chem. Biol. 26, 1716–1724 e1719 (2019).
doi: 10.1016/j.chembiol.2019.09.014
pubmed: 31631010
Woodley, K. T. & Collins, M. O. S-acylated Golga7b stabilises DHHC5 at the plasma membrane to regulate cell adhesion. EMBO Rep. 20, e47472 (2019).
doi: 10.15252/embr.201847472
pubmed: 31402609
pmcid: 6776912
Mitchell, D. A., Mitchell, G., Ling, Y., Budde, C. & Deschenes, R. J. Mutational analysis of Saccharomyces cerevisiae Erf2 reveals a two-step reaction mechanism for protein palmitoylation by DHHC enzymes. J. Biol. Chem. 285, 38104–38114 (2010).
doi: 10.1074/jbc.M110.169102
pubmed: 20851885
pmcid: 2992244
Jennings, B. C. & Linder, M. E. DHHC protein S-acyltransferases use similar ping-pong kinetic mechanisms but display different acyl-CoA specificities. J. Biol. Chem. 287, 7236–7245 (2012).
doi: 10.1074/jbc.M111.337246
pubmed: 22247542
pmcid: 3293542
Salaun, C., Locatelli, C., Zmuda, F., Cabrera Gonzalez, J. & Chamberlain, L. H. Accessory proteins of the zDHHC family of S-acylation enzymes. J. Cell Sci. 133, jcs251819 (2020).
doi: 10.1242/jcs.251819
pubmed: 33203738
Yang, W., Di Vizio, D., Kirchner, M., Steen, H. & Freeman, M. R. Proteome scale characterization of human S-acylated proteins in lipid raft-enriched and non-raft membranes. Mol. Cell Proteom. 9, 54–70 (2010).
doi: 10.1074/mcp.M800448-MCP200
Abrami, L. et al. Identification and dynamics of the human ZDHHC16–ZDHHC6 palmitoylation cascade. eLife 6, e27826 (2017).
doi: 10.7554/eLife.27826
pubmed: 28826475
pmcid: 5582869
Hamel, L. D., Deschenes, R. J. & Mitchell, D. A. A fluorescence-based assay to monitor autopalmitoylation of zDHHC proteins applicable to high-throughput screening. Anal. Biochem. 460, 1–8 (2014).
doi: 10.1016/j.ab.2014.05.013
pubmed: 24878334
pmcid: 6445550
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
doi: 10.1038/nmeth.4193
pubmed: 28250466
pmcid: 5494038
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
doi: 10.1038/nmeth.4169
pubmed: 28165473
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
doi: 10.1002/jcc.20084
pubmed: 15264254
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
doi: 10.7554/eLife.42166
pubmed: 30412051
pmcid: 6250425
Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020).
doi: 10.1038/s41592-020-00990-8
pubmed: 33257830
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
doi: 10.1002/pro.3235
pubmed: 28710774
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
doi: 10.1038/s41586-021-03819-2
pubmed: 34265844
pmcid: 8371605
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
doi: 10.1107/S0907444904019158
pubmed: 15572765
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
doi: 10.1107/S0907444909052925
pubmed: 20124702
pmcid: 2815670
Johnson, M. et al. NCBI BLAST: a better web interface. Nucleic Acids Res. 36, W5–9 (2008).
doi: 10.1093/nar/gkn201
pubmed: 18440982
pmcid: 2447716