Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structure of p300 in complex with acyl-CoA variants

Nature Chemical Biology volume 13, pages 21–29 (2017)Cite this article

Subjects

Abstract

Histone acetylation plays an important role in transcriptional activation. Histones are also modified by chemically diverse acylations that are frequently deposited by p300, a transcriptional coactivator that uses a number of different acyl-CoA cofactors. Here we report that while p300 is a robust acetylase, its activity gets weaker with increasing acyl-CoA chain length. Crystal structures of p300 in complex with propionyl-, crotonyl-, or butyryl-CoA show that the aliphatic portions of these cofactors are bound in the lysine substrate-binding tunnel in a conformation that is incompatible with substrate transfer. Lysine substrate binding is predicted to remodel the acyl-CoA ligands into a conformation compatible with acyl-chain transfer. This remodeling requires that the aliphatic portion of acyl-CoA be accommodated in a hydrophobic pocket in the enzymes active site. The size of the pocket and its aliphatic nature exclude long-chain and charged acyl-CoA variants, presumably explaining the cofactor preference for p300.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Acyltransferase activity of p300.
Figure 2: Structure of p300 in complex with acyl-CoA variants.
Figure 3: Comparison of the structure of p300 in complex with different acyl-CoA ligands.
Figure 4: Comparison of p300 with GNAT acyltransferases.
Figure 5: Analysis of the impact of p300 mutagenesis on the histone acylation profile.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank

References

  1. Janke, R., Dodson, A.E. & Rine, J. Metabolism and epigenetics. Annu. Rev. Cell Dev. Biol. 31, 473–496 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Roth, S.Y., Denu, J.M. & Allis, C.D. Histone acetyltransferases. Annu. Rev. Biochem. 70, 81–120 (2001).

    Article  CAS  PubMed  Google Scholar 

  3. Dhalluin, C. et al. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399, 491–496 (1999).

    Article  CAS  PubMed  Google Scholar 

  4. Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature 403, 41–45 (2000).

    Article  CAS  PubMed  Google Scholar 

  5. Chen, Y. et al. Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol. Cell. Proteomics 6, 812–819 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. Tan, M. et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146, 1016–1028 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Yang, Y.Y., Grammel, M. & Hang, H.C. Identification of lysine acetyltransferase p300 substrates using 4-pentynoyl-coenzyme A and bioorthogonal proteomics. Bioorg. Med. Chem. Lett. 21, 4976–4979 (2011).

    Article  CAS  PubMed  Google Scholar 

  8. Xie, Z. et al. Lysine succinylation and lysine malonylation in histones. Mol. Cell. Proteomics 11, 100–107 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Dai, L. et al. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat. Chem. Biol. 10, 365–370 (2014).

    Article  CAS  PubMed  Google Scholar 

  10. Tan, M. et al. Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. Cell Metab. 19, 605–617 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Zhang, Z. et al. Identification of lysine succinylation as a new post-translational modification. Nat. Chem. Biol. 7, 58–63 (2011).

    Article  CAS  PubMed  Google Scholar 

  12. Peng, C. et al. The first identification of lysine malonylation substrates and its regulatory enzyme. Mol. Cell Proteomics 10 http://dx.doi.org/10.1074/mcp.M111.012658 (2011).

    Article  Google Scholar 

  13. Moellering, R.E. & Cravatt, B.F. Functional lysine modification by an intrinsically reactive primary glycolytic metabolite. Science 341, 549–553 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Xie, Z. et al. Metabolic regulation of gene expression by histone lysine β-hydroxybutyrylation. Mol. Cell 62, 194–206 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Huang, H., Lin, S., Garcia, B.A. & Zhao, Y. Quantitative proteomic analysis of histone modifications. Chem. Rev. 115, 2376–2418 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Cai, L., Sutter, B.M., Li, B. & Tu, B.P. Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol. Cell 42, 426–437 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Lin, H., Su, X. & He, B. Protein lysine acylation and cysteine succination by intermediates of energy metabolism. ACS Chem. Biol. 7, 947–960 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Flynn, E.M. et al. A subset of human bromodomains recognizes butyryllysine and crotonyllysine histone peptide modifications. Structure 23, 1801–1814 (2015).

    Article  CAS  PubMed  Google Scholar 

  19. Goudarzi, A. et al. Dynamic competing histone H4 K5K8 acetylation and butyrylation are hallmarks of highly active gene promoters. Mol. Cell 62, 169–180 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Andrews, F.H. et al. The Taf14 YEATS domain is a reader of histone crotonylation. Nat. Chem. Biol. 12, 396–398 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Li, Y. et al. Molecular coupling of histone crotonylation and active transcription by AF9 YEATS domain. Mol. Cell 62, 181–193 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Du, J. et al. Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science 334, 806–809 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Park, J. et al. SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways. Mol. Cell 50, 919–930 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Cheng, Z. et al. Molecular characterization of propionyllysines in non-histone proteins. Mol. Cell. Proteomics 8, 45–52 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Feldman, J.L., Baeza, J. & Denu, J.M. Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins. J. Biol. Chem. 288, 31350–31356 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Bao, X. et al. Identification of 'erasers' for lysine crotonylated histone marks using a chemical proteomics approach. eLife 3 (2014).

  27. Garrity, J., Gardner, J.G., Hawse, W., Wolberger, C. & Escalante-Semerena, J.C. N-lysine propionylation controls the activity of propionyl-CoA synthetase. J. Biol. Chem. 282, 30239–30245 (2007).

    Article  CAS  PubMed  Google Scholar 

  28. Smith, B.C. & Denu, J.M. Acetyl-lysine analog peptides as mechanistic probes of protein deacetylases. J. Biol. Chem. 282, 37256–37265 (2007).

    Article  CAS  PubMed  Google Scholar 

  29. Jiang, H. et al. SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine. Nature 496, 110–113 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Yuan, H. & Marmorstein, R. Histone acetyltransferases: rising ancient counterparts to protein kinases. Biopolymers 99, 98–111 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Allis, C.D. et al. New nomenclature for chromatin-modifying enzymes. Cell 131, 633–636 (2007).

    Article  CAS  PubMed  Google Scholar 

  32. Sabari, B.R. et al. Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Mol. Cell 58, 203–215 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hu, A., Britton, L.M. & Garcia, B.A. Investigating the specificity of histone acetyltransferase activity for producing rare modifications on histones using mass spectrometry. The 62nd Annual American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics (Baltimore, MD, 2014).

  34. Berndsen, C.E., Albaugh, B.N., Tan, S. & Denu, J.M. Catalytic mechanism of a MYST family histone acetyltransferase. Biochemistry 46, 623–629 (2007).

    Article  CAS  PubMed  Google Scholar 

  35. Leemhuis, H., Packman, L.C., Nightingale, K.P. & Hollfelder, F. The human histone acetyltransferase P/CAF is a promiscuous histone propionyltransferase. ChemBioChem 9, 499–503 (2008).

    Article  CAS  PubMed  Google Scholar 

  36. Ringel, A.E. & Wolberger, C. Structural basis for acyl-group discrimination by human Gcn5L2. Acta Crystallogr. D Struct. Biol. 72, 841–848 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Thompson, P.R. et al. Regulation of the p300 HAT domain via a novel activation loop. Nat. Struct. Mol. Biol. 11, 308–315 (2004).

    Article  CAS  PubMed  Google Scholar 

  38. Liu, X. et al. The structural basis of protein acetylation by the p300/CBP transcriptional coactivator. Nature 451, 846–850 (2008).

    Article  CAS  PubMed  Google Scholar 

  39. Delvecchio, M., Gaucher, J., Aguilar-Gurrieri, C., Ortega, E. & Panne, D. Structure of the p300 catalytic core and implications for chromatin targeting and HAT regulation. Nat. Struct. Mol. Biol. 20, 1040–1046 (2013).

    Article  CAS  PubMed  Google Scholar 

  40. Maksimoska, J., Segura-Peña, D., Cole, P.A. & Marmorstein, R. Structure of the p300 histone acetyltransferase bound to acetyl-coenzyme A and its analogues. Biochemistry 53, 3415–3422 (2014).

    Article  CAS  PubMed  Google Scholar 

  41. Thompson, P.R., Kurooka, H., Nakatani, Y. & Cole, P.A. Transcriptional coactivator protein p300. Kinetic characterization of its histone acetyltransferase activity. J. Biol. Chem. 276, 33721–33729 (2001).

    Article  CAS  PubMed  Google Scholar 

  42. Gould, T.A., Schweizer, H.P. & Churchill, M.E. Structure of the Pseudomonas aeruginosa acyl-homoserinelactone synthase LasI. Mol. Microbiol. 53, 1135–1146 (2004).

    Article  CAS  PubMed  Google Scholar 

  43. Watson, W.T., Minogue, T.D., Val, D.L., von Bodman, S.B. & Churchill, M.E. Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing. Mol. Cell 9, 685–694 (2002).

    Article  CAS  PubMed  Google Scholar 

  44. Carvalho, P.C., Hewel, J., Barbosa, V.C. & Yates, J.R. III. Identifying differences in protein expression levels by spectral counting and feature selection. Genet. Mol. Res. 7, 342–356 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Karukurichi, K.R. & Cole, P.A. Probing the reaction coordinate of the p300/CBP histone acetyltransferase with bisubstrate analogs. Bioorg. Chem. 39, 42–47 (2011).

    Article  CAS  PubMed  Google Scholar 

  46. Zhang, X. et al. Catalytic mechanism of histone acetyltransferase p300: from the proton transfer to acetylation reaction. J. Phys. Chem. B 118, 2009–2019 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Rousseaux, S. & Khochbin, S. Histone acylation beyond acetylation: aerra incognita in chromatin biology. Cell J. 17, 1–6 (2015).

    PubMed  PubMed Central  Google Scholar 

  48. Yang, C. et al. Labeling lysine acetyltransferase substrates with engineered enzymes and functionalized cofactor surrogates. J. Am. Chem. Soc. 135, 7791–7794 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. King, M.T. & Reiss, P.D. Separation and measurement of short-chain coenzyme-A compounds in rat liver by reversed-phase high-performance liquid chromatography. Anal. Biochem. 146, 173–179 (1985).

    Article  CAS  PubMed  Google Scholar 

  50. Hosokawa, Y., Shimomura, Y., Harris, R.A. & Ozawa, T. Determination of short-chain acyl-coenzyme A esters by high-performance liquid chromatography. Anal. Biochem. 153, 45–49 (1986).

    Article  CAS  PubMed  Google Scholar 

  51. Luger, K., Rechsteiner, T.J. & Richmond, T.J. Preparation of nucleosome core particle from recombinant histones. Methods Enzymol. 304, 3–19 (1999).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank the staff of ESRF and EMBL-Grenoble for assistance and support in using beamlines ID29, 23-1 and 23-2 and the HTX facility. We thank L. Signor (IBS, Grenoble) and P. Phapale (EMBL) for MS analysis. This work used the platforms of the Grenoble Instruct centre (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05-02) and GRAL (ANR-10-LABX-49-01) within the Grenoble Partnership for Structural Biology (PSB). Z.K. was supported by a fellowship from the EMBL Interdisciplinary Postdoc Programme under Marie Skłodowska-Curie actions Cofund (grant agreement number 291772). This work was supported by the ANR Grant Episperm3 (ANR-15-CE12- 0005-02) to S. Khochbin and D.P. and the Worldwide Cancer Research foundation (grant #16-0280) to D.P. Work in S. Khochbin's laboratory is supported by INCa, Fondation pour la Recherche Médicale and Fondation ARC. Work in Y.Z.'s laboratory is supported by NIH grants GM105933, DK107868 and GM115961.

Author information

Author notes

  1. Zuzanna Kaczmarska and Esther Ortega: These authors contributed equally to this work.

Authors and Affiliations

  1. European Molecular Biology Laboratory, Grenoble, France

    Zuzanna Kaczmarska, Esther Ortega, José A Márquez & Daniel Panne

  2. Université Grenoble Alpes, Institut Albert Bonniot, Grenoble, France

    Afsaneh Goudarzi & Saadi Khochbin

  3. Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois, USA

    He Huang, Sunjoo Kim & Yingming Zhao

Authors
  1. Zuzanna Kaczmarska
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Esther Ortega
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Afsaneh Goudarzi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. He Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sunjoo Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. José A Márquez
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yingming Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Saadi Khochbin
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Daniel Panne
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Z.K. performed the structure determination of p300 under supervision of J.A.M. and D.P. E.O. and Z.K. performed biochemical assays. E.O. prepared the constructs and performed protein expression and purification. A.G. performed the IP–HAT experiments under the supervision of S. Khochbin. H.H. and S. Kim performed MS experiments under the supervision of Y.Z. D.P. designed and coordinated the project, advised and assisted on all aspects of the project and wrote the manuscript. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Daniel Panne.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Table 1 and Supplementary Figures 1–7. (PDF 1196 kb)

Supplementary Note

Annotated MS/MS spectra of for histone KAc from experiments shown in Figure 5. (PDF 2579 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kaczmarska, Z., Ortega, E., Goudarzi, A. et al. Structure of p300 in complex with acyl-CoA variants. Nat Chem Biol 13, 21–29 (2017). https://doi.org/10.1038/nchembio.2217

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.2217

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing