CoChat
Sign Up
Cited by 38Protein Kinase Regulation and GTPase SignalingCellular transport and secretionLipid Membrane Structure and Behavior

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Regulation of RAS palmitoyltransferases by accessory proteins and palmitoylation

Open access
Yang, Anlan, Liu, Shengjie, Zhang, Yuqi, Chen, Jia, Fan, Yujing, Wang, Fengxiang, Zou, Yilong, Feng, Shan, Wu, Jianping, Hu, Qi·2024·Nature Structural & Molecular Biology
DOI 10.1038/s41594-023-01183-5

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

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.

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 · 10.1038/s41594-023-01183-5

Cites

2 of 2 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: 38

  1. 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
  2. Campbell, S. L. & Philips, M. R. Post-translational modification of RAS proteins. Curr. Opin. Struct. Biol. 71, 180–192 (2021). · DOI
  3. Rocks, O. et al. An acylation cycle regulates localization and activity of palmitoylated Ras isoforms. Science 307, 1746–1752 (2005). · DOI
  4. 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
  5. 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
  6. 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
  7. Jiang, H. et al. Protein lipidation: occurrence, mechanisms, biological functions, and enabling technologies. Chem. Rev. 118, 919–988 (2018). · DOI
  8. Rana, M. S. et al. Fatty acyl recognition and transfer by an integral membrane S-acyltransferase. Science 359, eaao6326 (2018). · DOI
  9. 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. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. Ahearn, I. M. et al. FKBP12 binds to acylated H-ras and promotes depalmitoylation. Mol. Cell 41, 173–185 (2011). · DOI
  18. 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
  19. 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
  20. 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
  21. 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
  22. Ko, P. J. et al. A ZDHHC5–GOLGA7 protein acyltransferase complex promotes nonapoptotic cell death. Cell Chem. Biol. 26, 1716–1724 e1719 (2019). · DOI
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. Abrami, L. et al. Identification and dynamics of the human ZDHHC16–ZDHHC6 palmitoylation cascade. eLife 6, e27826 (2017). · DOI
  29. 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
  30. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). · DOI
  31. 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 · Paper page
  32. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). · DOI
  33. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018). · DOI
  34. 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
  35. Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018). · DOI · Paper page
  36. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004). · DOI · Paper page
  37. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010). · DOI · Paper page
  38. Johnson, M. et al. NCBI BLAST: a better web interface. Nucleic Acids Res. 36, W5–9 (2008). · DOI

Metadata

Authors
Yang, A., Liu, S., Zhang, Y., Chen, J., Fan, Y., Wang, F., Zou, Y., Feng, S., Wu, J., & Hu, Q.
Affiliations
  • Westlake University (CN)
  • Fudan University (CN)
Corresponding author
  • Wu, Jianping
  • Hu, Qi
ORCID
Venue
Nature Structural & Molecular Biology
Publisher
Springer Science and Business Media LLC
Published
2024-01-05
Volume
31
Issue
3
Pages
436-446
ISSN
  • 1545-9985 (ISSN-L)
  • 1545-9993
DOI
10.1038/s41594-023-01183-5
OpenAlex
W4390615537
Cited by
38
References
2
Citations by year
2026: 15 · 2025: 13 · 2024: 8
FWCI
4.91
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Structural & Molecular Biology (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
Funders
Westlake University
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
Keywords
cysteine palmitoylation, accessory proteins, phospholipid binding, arginine-rich region, HRAS, NRAS, cryo-EM structure, protein complex structure
MeSH terms
Acyltransferases, Humans, Membrane Proteins, Saccharomyces cerevisiae, Cryoelectron Microscopy, Lipoylation

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