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:

Cyclic AMP regulation of protein lysine acetylation in Mycobacterium tuberculosis

Nature Structural & Molecular Biology volume 19, pages 811–818 (2012)Cite this article

Subjects

Abstract

Protein lysine acetylation networks can regulate central processes such as carbon metabolism and gene expression in bacteria. In Escherichia coli, cyclic AMP (cAMP) regulates protein lysine acetyltransferase (PAT) activity at the transcriptional level, but in Mycobacterium tuberculosis, fusion of a cyclic nucleotide-binding domain to a Gcn5-like PAT domain enables direct cAMP control of protein acetylation. Here we describe the allosteric activation mechanism of M. tuberculosis PAT. The crystal structures of the autoinhibited and cAMP-activated PAT reveal that cAMP binds to a cryptic site in the regulatory domain that is over 32 Å from the catalytic site. An extensive conformational rearrangement relieves this autoinhibition by means of a substrate-mimicking lid that covers the protein-substrate binding surface. A steric double latch couples the domains by harnessing a classic, cAMP-mediated conformational switch. The structures suggest general features that enable the evolution of long-range communication between linked domains.

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: A double steric latch autoinhibits Mt-PatA.
Figure 2: Crystal structure of the active form of Mt-PatA.
Figure 3: Mechanisms of interdomain communication.
Figure 4: Mutants support a two-state model for Mt-PatA activation.
Figure 5: The open lid in the active state uncovers a cavity for the substrate lysine.
Figure 6: A steric double latch regulates Mt-PatA.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

References

  1. Frankel, A.D. & Kim, P.S. Modular structure of transcription factors: implications for gene regulation. Cell 65, 717–719 (1991).

    Article  CAS  Google Scholar 

  2. Dorit, R.L. & Gilbert, W. The limited universe of exons. Curr. Opin. Genet. Dev. 1, 464–469 (1991).

    Article  CAS  Google Scholar 

  3. Long, M., de Souza, S.J. & Gilbert, W. Evolution of the intron-exon structure of eukaryotic genes. Curr. Opin. Genet. Dev. 5, 774–778 (1995).

    Article  CAS  Google Scholar 

  4. Geer, L.Y., Domrachev, M., Lipman, D.J. & Bryant, S.H. CDART: protein homology by domain architecture. Genome Res. 12, 1619–1623 (2002).

    Article  CAS  Google Scholar 

  5. Marcotte, E.M., Pellegrini, M., Thompson, M.J., Yeates, T.O. & Eisenberg, D. A combined algorithm for genome-wide prediction of protein function. Nature 402, 83–86 (1999).

    Article  CAS  Google Scholar 

  6. Kuriyan, J. & Eisenberg, D. The origin of protein interactions and allostery in colocalization. Nature 450, 983–990 (2007).

    Article  CAS  Google Scholar 

  7. Kuriyan, J. & Cowburn, D. Modular peptide recognition domains in eukaryotic signaling. Annu. Rev. Biophys. Biomol. Struct. 26, 259–288 (1997).

    Article  CAS  Google Scholar 

  8. Hu, L.I., Lima, B.P. & Wolfe, A.J. Bacterial protein acetylation: the dawning of a new age. Mol. Microbiol. 77, 15–21 (2010).

    Article  CAS  Google Scholar 

  9. Kim, G.W. & Yang, X.J. Comprehensive lysine acetylomes emerging from bacteria to humans. Trends Biochem. Sci. 36, 211–220 (2011).

    Article  CAS  Google Scholar 

  10. Schwer, B., Bunkenborg, J., Verdin, R.O., Andersen, J.S. & Verdin, E. Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2. Proc. Natl. Acad. Sci. USA 103, 10224–10229 (2006).

    Article  CAS  Google Scholar 

  11. Hirschey, M.D., Shimazu, T., Huang, J.Y., Schwer, B. & Verdin, E. SIRT3 regulates mitochondrial protein acetylation and intermediary metabolism. Cold Spring Harb. Symp. Quant. Biol. 76, 267–277 (2011).

    Article  CAS  Google Scholar 

  12. Yu, B.J., Kim, J.A., Moon, J.H., Ryu, S.E. & Pan, J.G. The diversity of lysine-acetylated proteins in Escherichia coli. J. Microbiol. Biotechnol. 18, 1529–1536 (2008).

    CAS  PubMed  Google Scholar 

  13. Wang, Q. et al. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 327, 1004–1007 (2010).

    Article  CAS  Google Scholar 

  14. Zhang, J. et al. Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol. Cell. Proteomics 8, 215–225 (2009).

    Article  CAS  Google Scholar 

  15. Thao, S. & Escalante-Semerena, J.C. Control of protein function by reversible Nɛ-lysine acetylation in bacteria. Curr. Opin. Microbiol. 14, 200–204 (2011).

    Article  CAS  Google Scholar 

  16. Castaño-Cerezo, S., Bernal, V., Blanco-Catala, J., Iborra, J.L. & Canovas, M. cAMP-CRP co-ordinates the expression of the protein acetylation pathway with central metabolism in Escherichia coli. Mol. Microbiol. 82, 1110–1128 (2011).

    Article  Google Scholar 

  17. Nanchen, A., Schicker, A., Revelles, O. & Sauer, U. Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli. J. Bacteriol. 190, 2323–2330 (2008).

    Article  CAS  Google Scholar 

  18. Nambi, S., Basu, N. & Visweswariah, S.S. cAMP-regulated protein lysine acetylases in mycobacteria. J. Biol. Chem. 285, 24313–24323 (2010).

    Article  CAS  Google Scholar 

  19. Xu, H., Hegde, S.S. & Blanchard, J.S. Reversible acetylation and inactivation of Mycobacterium tuberculosis acetyl-CoA synthetase is dependent on cAMP. Biochemistry 50, 5883–5892 (2011).

    Article  CAS  Google Scholar 

  20. Nyström, T. & Neidhardt, F.C. Expression and role of the universal stress protein, UspA, of Escherichia coli during growth arrest. Mol. Microbiol. 11, 537–544 (1994).

    Article  Google Scholar 

  21. Crosby, H.A., Pelletier, D.A., Hurst, G.B. & Escalante-Semerena, J.C. System-wide studies of N-lysine acetylation in Rhodopseudomonas palustris reveals substrate specificity of protein acetyltransferases. J. Biol. Chem. 287, 15590–15601 (2012).

    Article  CAS  Google Scholar 

  22. Vetting, M.W. et al. Structure and functions of the GNAT superfamily of acetyltransferases. Arch. Biochem. Biophys. 433, 212–226 (2005).

    Article  CAS  Google Scholar 

  23. Fraser, J.S. et al. Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc. Natl. Acad. Sci. USA 108, 16247–16252 (2011).

    Article  CAS  Google Scholar 

  24. Lang, P.T. et al. Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci. 19, 1420–1431 (2010).

    Article  CAS  Google Scholar 

  25. 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  Google Scholar 

  26. Nambi, S., Badireddy, S., Visweswariah, S.S. & Anand, G.S. Cyclic AMP–induced conformational changes in mycobacterial protein acetyltransferases. J. Biol. Chem. 287, 18115–18129 (2012).

    Article  CAS  Google Scholar 

  27. Kornev, A.P., Taylor, S.S. & Ten Eyck, L.F. A generalized allosteric mechanism for cis-regulated cyclic nucleotide binding domains. PLoS Comput. Biol. 4, e1000056 (2008).

    Article  Google Scholar 

  28. Popovych, N., Tzeng, S.R., Tonelli, M., Ebright, R.H. & Kalodimos, C.G. Structural basis for cAMP-mediated allosteric control of the catabolite activator protein. Proc. Natl. Acad. Sci. USA 106, 6927–6932 (2009).

    Article  CAS  Google Scholar 

  29. Passner, J.M., Schultz, S.C. & Steitz, T.A. Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 Å resolution. J. Mol. Biol. 304, 847–859 (2000).

    Article  CAS  Google Scholar 

  30. Sharma, H., Yu, S., Kong, J., Wang, J. & Steitz, T.A. Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding. Proc. Natl. Acad. Sci. USA 106, 16604–16609 (2009).

    Article  CAS  Google Scholar 

  31. Kim, C., Xuong, N.H. & Taylor, S.S. Crystal structure of a complex between the catalytic and regulatory (RIα) subunits of PKA. Science 307, 690–696 (2005).

    Article  CAS  Google Scholar 

  32. Berman, H.M. et al. The cAMP binding domain: an ancient signaling module. Proc. Natl. Acad. Sci. USA 102, 45–50 (2005).

    Article  CAS  Google Scholar 

  33. Shenoy, A.R. & Visweswariah, S.S. New messages from old messengers: cAMP and mycobacteria. Trends Microbiol. 14, 543–550 (2006).

    Article  CAS  Google Scholar 

  34. Bai, G., Knapp, G.S. & McDonough, K.A. Cyclic AMP signalling in mycobacteria: redirecting the conversation with a common currency. Cell Microbiol. 13, 349–358 (2011).

    Article  Google Scholar 

  35. Muñoz-Elias, E.J. et al. Replication dynamics of Mycobacterium tuberculosis in chronically infected mice. Infect. Immun. 73, 546–551 (2005).

    Article  Google Scholar 

  36. Gill, W.P. et al. A replication clock for Mycobacterium tuberculosis. Nat. Med. 15, 211–214 (2009).

    Article  CAS  Google Scholar 

  37. Wayne, L.G. Synchronized replication of Mycobacterium tuberculosis. Infect. Immun. 17, 528–530 (1977).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Brent, M.M., Iwata, A., Carten, J., Zhao, K. & Marmorstein, R. Structure and biochemical characterization of protein acetyltransferase from Sulfolobus solfataricus. J. Biol. Chem. 284, 19412–19419 (2009).

    Article  CAS  Google Scholar 

  39. Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L. & Clardy, J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229, 105–124 (1993).

    Article  CAS  Google Scholar 

  40. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  41. Leslie, A.G.W. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 ESF-EAMCB Newslett. Protein Crystallogr. 26 (1992).

  42. Collaborative Computational Project, No. 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).

  43. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  Google Scholar 

  44. Langer, G., Cohen, S.X., Lamzin, V.S. & Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171–1179 (2008).

    Article  CAS  Google Scholar 

  45. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  Google Scholar 

  46. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article  CAS  Google Scholar 

  47. Murshudov, G.N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011).

    Article  CAS  Google Scholar 

  48. Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D Biol. Crystallogr. 62, 1002–1011 (2006).

    Article  Google Scholar 

  49. Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).

    Article  CAS  Google Scholar 

  50. Larkin, M.A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007).

    Article  CAS  Google Scholar 

  51. Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983).

    Article  CAS  Google Scholar 

  52. Pettersen, E.F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Holton, G. Meigs and J. Tanamachi at Beamline 8.3.1 at Lawrence Berkeley National Laboratory for help with X-ray data collection. We appreciate the support of the TB Structural Genomics Consortium. This work was supported by a postdoctoral research fellowship from the Canadian Institutes of Health Research to H.J.L. and US National Institutes of Health grants R01GM70962 and P01AI068135 to T.A.

Author information

Authors and Affiliations

  1. Department of Molecular and Cell Biology, University of California, Berkeley, California, USA

    Ho Jun Lee, P Therese Lang & Tom Alber

  2. QB3 Institute, University of California, Berkeley, California, USA

    Ho Jun Lee, P Therese Lang & Tom Alber

  3. Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA

    Sarah M Fortune

  4. Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    Christopher M Sassetti

  5. Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    Christopher M Sassetti

Authors
  1. Ho Jun Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. P Therese Lang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sarah M Fortune
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Christopher M Sassetti
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tom Alber
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

H.J.L. conducted all the biochemical and crystallographic studies. P.T.L. conducted the computational studies with Ringer. T.A., H.J.L., P.T.L. and C.M.S. wrote the manuscript. All authors designed analyses, discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Tom Alber.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 4404 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lee, H., Lang, P., Fortune, S. et al. Cyclic AMP regulation of protein lysine acetylation in Mycobacterium tuberculosis. Nat Struct Mol Biol 19, 811–818 (2012). https://doi.org/10.1038/nsmb.2318

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.2318

This article is cited by

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