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.

  • Review Article
  • Published:

Capturing cyclic nucleotides in action: snapshots from crystallographic studies

Nature Reviews Molecular Cell Biology volume 8, pages 63–73 (2007)Cite this article

Key Points

  • cyclic AMP and cyclic GMP are universal second messengers and are sensed by receptor proteins that contain cyclic nucleotide binding (CNB) domains.

  • In mammal, CNB domains are found in protein kinase A (PKA), protein kinase G (PKG), the guanine nucleotide-exchange factor Epac and cyclic-nucleotide-regulated ion channels. These receptor proteins mediate the wide range of biological effects that are controlled by cyclic nucleotides, including the regulation of gene transcription, cell adhesion and heart rhythm, mediating the biochemical processes that are fundamental to vision and scent, and the modulation of insulin secretion.

  • CNB domains are structurally conserved switch domains that consist of a central β-sandwich flanked at the N terminus by the N-terminal helical bundle and at the C terminus by the hinge helix and the lid.

  • Ligand binding induces conformational changes in that region of the β-sandwich that interacts directly with the phosphate-sugar moiety of the nucleotide. These changes are translated into a movement of the hinge and the lid, as well as of a rearrangement of the N-terminal helical bundle.

  • The structural changes that are induced by ligand binding are universal in CNB domains. They are coupled in an individual manner with protein activation in the different classes of cyclic nucleotide receptors.

Abstract

Fifty years ago, cyclic AMP was discovered as a second messenger of hormone action, heralding the age of signal transduction. Many cellular processes were found to be regulated by cAMP and the related cyclic GMP. Cyclic nucleotides function by binding to and activating their effectors — protein kinase A, protein kinase G, cyclic-nucleotide-regulated ion channels and the guanine nucleotide-exchange factor Epac. Recent structural insights have now made it possible to propose a general structural mechanism for how cyclic nucleotides regulate these proteins.

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: Cyclic nucleotide metabolism.
Figure 2: The first structure of a cyclic-nucleotide-binding domain.
Figure 3: Universal conformational changes in cyclic-nucleotide-binding domains following the binding of a cyclic nucleotide.
Figure 4: Model of cyclic-nucleotide-induced conformational changes.
Figure 5: The regulation of protein kinase A by cyclic AMP.
Figure 6: The regulation of cyclic-nucleotide-regulated ion channels by cyclic AMP.
Figure 7: The regulation of Epac by cyclic AMP.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Vaandrager, A. B. & de Jonge, H. R. Signalling by cGMP-dependent protein kinases. Mol. Cell. Biochem. 157, 23–30 (1996).

    Article  CAS  PubMed  Google Scholar 

  2. Craven, K. B. & Zagotta, W. N. CNG and HCN channels: two peas, one pod. Annu. Rev. Physiol. 68, 375–401 (2006).

    Article  CAS  PubMed  Google Scholar 

  3. Kaupp, U. B. & Seifert, R. Molecular diversity of pacemaker ion channels. Annu. Rev. Physiol. 63, 235–257 (2001).

    Article  CAS  PubMed  Google Scholar 

  4. Kaupp, U. B. & Seifert, R. Cyclic nucleotide-gated ion channels. Physiol. Rev. 82, 769–824 (2002).

    Article  CAS  PubMed  Google Scholar 

  5. Bos, J. L. Epac: a new cAMP target and new avenues in cAMP research. Nature Rev. Mol. Cell Biol. 4, 733–738 (2003).

    Article  CAS  Google Scholar 

  6. Seino, S. & Shibasaki, T. PKA-dependent and PKA-independent pathways for cAMP-regulated exocytosis. Physiol. Rev. 85, 1303–1342 (2005).

    Article  CAS  PubMed  Google Scholar 

  7. Beavo, J. A. & Brunton, L. L. Cyclic nucleotide research — still expanding after half a century. Nature Rev. Mol. Cell Biol. 3, 710–718 (2002).

    Article  CAS  Google Scholar 

  8. Rall, T. W., Sutherland, E. W. & Berthet, J. The relationship of epinephrine and glucagon to liver phosphorylase. IV. Effect of epinephrine and glucagon on the reactivation of phosphorylase in liver homogenates. J. Biol. Chem. 224, 463–475 (1957).

    CAS  PubMed  Google Scholar 

  9. Sutherland, E. W. & Rall, T. W. The properties of an adenine ribonucleotide produced with cellular particles, ATP, Mg++, and epinephrine or glucagon. J. Am. Chem. Soc. 79, 3608 (1957).

    Article  CAS  Google Scholar 

  10. Cook, W. H., Lipkin, D. & Markham, R. The formation of a cyclic dianhydrodiadenylic acid (I) by the alkaline degradation of adenosine-5′-triphosphoric acid (II). J. Am. Chem. Soc. 79, 3607–3608 (1957).

    Article  CAS  Google Scholar 

  11. Lipkin, D., Cook, W. H. & Markham, R. Adenosine-3′:5′-phosphoric acid: a proof of structure. J. Am. Chem. Soc. 81, 6198–6203 (1959).

    Article  CAS  Google Scholar 

  12. Sutherland, E. W., Rall, T. W. & Menon, T. Adenyl cyclase. I. Distribution, preperation, and properties. J. Biol. Chem. 237, 1220 (1961).

    Google Scholar 

  13. Taussig, R. & Gilman, A. G. Mammalian membrane-bound adenylyl cyclases. J. Biol. Chem. 270, 1–4 (1995).

    Article  CAS  PubMed  Google Scholar 

  14. Hanoune, J. & Defer, N. Regulation and role of adenylyl cyclase isoforms. Annu. Rev. Pharmacol. Toxicol. 41, 145–174 (2001).

    Article  CAS  PubMed  Google Scholar 

  15. Taussig, R. & Zimmermann, G. Type-specific regulation of mammalian adenylyl cyclases by G protein pathways. Adv. Sec. Mess. Phos. Res. 32, 81–98 (1998).

    Article  CAS  Google Scholar 

  16. Walsh, D. A., Perkins, J. P. & Krebs, E. G. Adensine 3′,5′-monophosphate-dependant protein kinase from rabbit skeletal muscle. J. Biol. Chem. 243, 3763–3765 (1968).

    CAS  PubMed  Google Scholar 

  17. Ashman, D. F., Lipton, R., Melicow, M. M. & Price, T. D. Isolation of adenosine 3′,5′-monophosphate and guanosine 3′,5′-monophosphate from rat urine. Biochem. Biophys. Res. Commun. 11, 330–334 (1963).

    Article  CAS  PubMed  Google Scholar 

  18. Kuo, J. F. & Greengard, P. Cyclic nucleotide-dependent protein kinases. IV. Widespread occurrence of adenosine 3′,5′-monophosphate-dependent protein kinase in various tissues and phyla of the animal kingdom. Proc. Natl Acad. Sci. USA 64, 1349–1355 (1969).

    Article  CAS  PubMed  Google Scholar 

  19. Kuo, J. F. & Greengard, P. Cyclic nucleotide-dependent protein kinases. VI. Isolation and partial purification of a protein kinase activated by guanosine 3′,5′-monophosphate. J. Biol. Chem. 245, 2493–2498 (1970).

    CAS  PubMed  Google Scholar 

  20. Yuen, P. S. & Garbers, D. L. Guanylyl cyclase-linked receptors. Annu. Rev. Neurosci. 15, 193–225 (1992).

    Article  CAS  PubMed  Google Scholar 

  21. Currie, M. G. et al. Bioactive cardiac substances: potent vasorelaxant activity in mammalian atria. Science 221, 71–73 (1983).

    Article  CAS  PubMed  Google Scholar 

  22. Furchgott, R. F. & Zawadzki, J. V. The obligatory role of endothelial cells in the relaxation of arterial smooth muscle by acetylcholine. Nature 288, 373–376 (1980).

    Article  CAS  PubMed  Google Scholar 

  23. Palmer, R. M., Ferrige, A. G. & Moncada, S. Nitric oxide release accounts for the biological activity of endothelium-derived relaxing factor. Nature 327, 524–526 (1987).

    Article  CAS  PubMed  Google Scholar 

  24. Ignarro, L. J., Buga, G. M., Wood, K. S., Byrns, R. E. & Chaudhuri, G. Endothelium-derived relaxing factor produced and released from artery and vein is nitric oxide. Proc. Natl Acad. Sci. USA 84, 9265–9269 (1987).

    Article  CAS  PubMed  Google Scholar 

  25. Friebe, A. & Koesling, D. Regulation of nitric oxide-sensitive guanylyl cyclase. Circ. Res. 93, 96–105 (2003).

    Article  CAS  PubMed  Google Scholar 

  26. Beavo, J. A., Conti, M. & Heaslip, R. J. Multiple cyclic nucleotide phosphodiesterases. Mol. Pharmacol. 46, 399–405 (1994).

    CAS  PubMed  Google Scholar 

  27. Manganiello, V. C., Murata, T., Taira, M., Belfrage, P. & Degerman, E. Diversity in cyclic nucleotide phosphodiesterase isoenzyme families. Arch. Biochem. Biophys. 322, 1–13 (1995).

    Article  CAS  PubMed  Google Scholar 

  28. Aravind, L. & Ponting, C. P. The GAF domain: an evolutionary link between diverse phototransducing proteins. Trends Biochem. Sci. 22, 458–459 (1997).

    Article  CAS  PubMed  Google Scholar 

  29. Martinez, S. E., Beavo, J. A. & Hol, W. G. GAF domains: two-billion-year-old molecular switches that bind cyclic nucleotides. Mol. Interv. 2, 317–323 (2002).

    Article  CAS  PubMed  Google Scholar 

  30. Zoraghi, R., Corbin, J. D. & Francis, S. H. Properties and functions of GAF domains in cyclic nucleotide phosphodiesterases and other proteins. Mol. Pharmacol. 65, 267–278 (2004).

    Article  CAS  PubMed  Google Scholar 

  31. Gross-Langenhoff, M., Hofbauer, K., Weber, J., Schultz, A. & Schultz, J. E. cAMP is a ligand for the tandem GAF domain of human phosphodiesterase 10 and cGMP for the tandem GAF domain of phosphodiesterase 11. J. Biol. Chem. 281, 2841–2846 (2006).

    Article  CAS  PubMed  Google Scholar 

  32. Martinez, S. E. et al. The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding. Proc. Natl Acad. Sci. USA 99, 13260–13265 (2002).

    Article  CAS  PubMed  Google Scholar 

  33. Martinez, S. E. et al. Crystal structure of the tandem GAF domains from a cyanobacterial adenylyl cyclase: modes of ligand binding and dimerization. Proc. Natl Acad. Sci. USA 102, 3082–3087 (2005).

    Article  CAS  PubMed  Google Scholar 

  34. Fesenko, E. E., Kolesnikov, S. S. & Lyubarsky, A. L. Induction by cyclic GMP of cationic conductance in plasma membrane of retinal rod outer segment. Nature 313, 310–313 (1985).

    Article  CAS  PubMed  Google Scholar 

  35. Miki, N., Keirns, J. J., Marcus, F. R., Freeman, J. & Bitensky, M. W. Regulation of cyclic nucleotide concentrations in photoreceptors: an ATP-dependent stimulation of cyclic nucleotide phosphodiesterase by light. Proc. Natl Acad. Sci. USA 70, 3820–3824 (1973).

    Article  CAS  PubMed  Google Scholar 

  36. Haynes, L. & Yau, K. W. Cyclic GMP-sensitive conductance in outer segment membrane of catfish cones. Nature 317, 61–64 (1985).

    Article  CAS  PubMed  Google Scholar 

  37. Cook, N. J., Hanke, W. & Kaupp, U. B. Identification, purification, and functional reconstitution of the cyclic GMP-dependent channel from rod photoreceptors. Proc. Natl Acad. Sci. USA 84, 585–589 (1987).

    Article  CAS  PubMed  Google Scholar 

  38. Nakamura, T. & Gold, G. H. A cyclic nucleotide-gated conductance in olfactory receptor cilia. Nature 325, 442–444 (1987).

    Article  CAS  PubMed  Google Scholar 

  39. Kaupp, U. B. et al. Primary structure and functional expression from complementary DNA of the rod photoreceptor cyclic GMP-gated channel. Nature 342, 762–766 (1989).

    Article  CAS  PubMed  Google Scholar 

  40. de Rooij, J. et al. Epac is a Rap1 guanine-nucleotide-exchange factor directly activated by cyclic AMP. Nature 396, 474–477 (1998).

    Article  CAS  PubMed  Google Scholar 

  41. Kawasaki, H. et al. A family of cAMP-binding proteins that directly activate Rap1. Science 282, 2275–2279 (1998).

    Article  CAS  PubMed  Google Scholar 

  42. McKay, D. B. & Steitz, T. A. Structure of catabolite gene activator protein at 2. 9 Å resolution suggests binding to left-handed B-DNA. Nature 290, 744–749 (1981). The first structure of a CNB domain; that of the bacterial protein CAP.

    Article  CAS  PubMed  Google Scholar 

  43. Emmer, M., deCrombrugghe, B., Pastan, I. & Perlman, R. Cyclic AMP receptor protein of E. coli: its role in the synthesis of inducible enzymes. Proc. Natl Acad. Sci. USA 66, 480–487 (1970).

    Article  CAS  PubMed  Google Scholar 

  44. Kolb, A., Busby, S., Buc, H., Garges, S. & Adhya, S. Transcriptional regulation by cAMP and its receptor protein. Annu. Rev. Biochem. 62, 749–795 (1993).

    Article  CAS  PubMed  Google Scholar 

  45. Bell, A. et al. Mutations that alter the ability of the Escherichia coli cyclic AMP receptor protein to activate transcription. Nucleic Acids Res. 18, 7243–7250 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Aiba, H., Fujimoto, S. & Ozaki, N. Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein. Nucleic Acids Res. 10, 1345–1361 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Cossart, P. & Gicquel-Sanzey, B. Cloning and sequence of the crp gene of Escherichia coli K12. Nucleic Acids Res. 10, 1363–1378 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. McKay, D. B., Weber, I. T. & Steitz, T. A. Structure of catabolite gene activator protein at 2.9-Å resolution. Incorporation of amino acid sequence and interactions with cyclic AMP. J. Biol. Chem. 257, 9518–9524 (1982).

    CAS  PubMed  Google Scholar 

  49. Takio, K., Smith, S. B., Krebs, E. G., Walsh, K. A. & Titani, K. Primary structure of the regulatory subunit of type II cAMP-dependent protein kinase from bovine cardiac muscle. Proc. Natl Acad. Sci. USA 79, 2544–2548 (1982).

    Article  CAS  PubMed  Google Scholar 

  50. Titani, K. et al. Amino acid sequence of the regulatory subunit of bovine type I adenosine cyclic 3′,5′-phosphate dependent protein kinase. Biochemistry 23, 4193–4199 (1984).

    Article  CAS  PubMed  Google Scholar 

  51. Takio, K. et al. Guanosine cyclic 3′,5′-phosphate dependent protein kinase, a chimeric protein homologous with two separate protein families. Biochemistry 23, 4207–4218 (1984).

    Article  CAS  PubMed  Google Scholar 

  52. Weber, I. T., Takio, K., Titani, K. & Steitz, T. A. The cAMP-binding domains of the regulatory subunit of cAMP-dependent protein kinase and the catabolite gene activator protein are homologous. Proc. Natl Acad. Sci. USA 79, 7679–7683 (1982).

    Article  CAS  PubMed  Google Scholar 

  53. Corbin, J. D. et al. Studies on the properties and mode of action of the purified regulatory subunit of bovine heart adenosine 3′:5′-monophosphate-dependent protein kinase. J. Biol. Chem. 253, 3997–4003 (1978).

    CAS  PubMed  Google Scholar 

  54. Su, Y. et al. Regulatory subunit of protein kinase A: structure of deletion mutant with cAMP binding domains. Science 269, 807–813 (1995).

    Article  CAS  PubMed  Google Scholar 

  55. Diller, T. C., Madhusudan, Xuong, N. H. & Taylor, S. S. Molecular basis for regulatory subunit diversity in cAMP-dependent protein kinase: crystal structure of the type II β regulatory subunit. Structure 9, 73–82 (2001). References 54 and 55 describe the structure of the regulatory subunit type I and type II, respectively.

    Article  CAS  PubMed  Google Scholar 

  56. 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). Structure of the complex between the regulatory subunit and the catalytic subunit of PKA.

    Article  CAS  PubMed  Google Scholar 

  57. Rehmann, H. et al. Structure and regulation of the cAMP-binding domains of Epac2. Nature Struct. Biol. 10, 26–32 (2003). First structure of a CNB domain in the absence of cyclic nucleotide; the hinge model was first presented here.

    Article  CAS  PubMed  Google Scholar 

  58. Rehmann, H., Das, J., Knipscheer, P., Wittinghofer, A. & Bos, J. L. Structure of the cyclic-AMP-responsive exchange factor Epac2 in its auto-inhibited state. Nature 439, 625–628 (2006).

    Article  CAS  PubMed  Google Scholar 

  59. Zagotta, W. N. et al. Structural basis for modulation and agonist specificity of HCN pacemaker channels. Nature 425, 200–205 (2003).

    Article  CAS  PubMed  Google Scholar 

  60. Clayton, G. M., Silverman, W. R., Heginbotham, L. & Morais-Cabral, J. H. Structural basis of ligand activation in a cyclic nucleotide regulated potassium channel. Cell 119, 615–627 (2004). References 59 and 60 describe the structures of CNB domains from cyclic-nucleotide-regulated ion channels.

    Article  CAS  PubMed  Google Scholar 

  61. Shabb, J. B. & Corbin, J. D. Cyclic nucleotide-binding domains in proteins having diverse functions. J. Biol. Chem. 267, 5723–5726 (1992).

    CAS  PubMed  Google Scholar 

  62. Canaves, J. M. & Taylor, S. S. Classification and phylogenetic analysis of the cAMP-dependent protein kinase regulatory subunit family. J. Mol. Evol. 54, 17–19 (2002).

    Article  CAS  PubMed  Google Scholar 

  63. Rehmann, H., Schwede, F., Doskeland, S. O., Wittinghofer, A. & Bos, J. L. Ligand-mediated activation of the cAMP-responsive guanine nucleotide exchange factor Epac. J. Biol. Chem. 278, 38548–38556 (2003).

    Article  CAS  Google Scholar 

  64. Enserink, J. M. et al. A novel Epac-specific cAMP analogue demonstrates independent regulation of Rap1 and ERK. Nature Cell Biol. 4, 901–906 (2002).

    Article  CAS  PubMed  Google Scholar 

  65. Weber, I. T., Shabb, J. B. & Corbin, J. D. Predicted structures of the cGMP binding domains of the cGMP-dependent protein kinase: a key alanine/threonine difference in evolutionary divergence of cAMP and cGMP binding sites. Biochemistry 28, 6122–6127 (1989).

    Article  CAS  PubMed  Google Scholar 

  66. Weber, I. T. & Steitz, T. A. Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 Å resolution. J. Mol. Biol. 198, 311–326 (1987).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  68. Rehmann, H., Rueppel, A., Bos, J. L. & Wittinghofer, A. Communication between the regulatory and the catalytic region of the cAMP-responsive guanine nucleotide exchange factor Epac. J. Biol. Chem. 278, 23508–23514 (2003).

    Article  CAS  PubMed  Google Scholar 

  69. Beavo, J. A., Bechtel, P. J. & Krebs, E. G. Mechanisms of control for cAMP-dependent protein kinase from skeletal muscle. Adv. Cyclic Nucleotide Res. 5, 241–251 (1975).

    CAS  PubMed  Google Scholar 

  70. Saraswat, L. D., Ringheim, G. E., Bubis, J. & Taylor, S. S. Deletion mutants as probes for localizing regions of subunit interaction in cAMP-dependent protein kinase. J. Biol. Chem. 263, 18241–18246 (1988).

    CAS  PubMed  Google Scholar 

  71. Knighton, D. R. et al. Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science 253, 414–420 (1991).

    Article  CAS  PubMed  Google Scholar 

  72. Knighton, D. R. et al. Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science 253, 407–414 (1991). References 71 and 72 describe the structure of the catalytic subunit of PKA, which represents the first structure of a kinase domain.

    Article  CAS  PubMed  Google Scholar 

  73. Feramisco, J. R. & Krebs, E. G. Inhibition of cyclic AMP-dependent protein kinase by analogues of a synthetic peptide substrate. J. Biol. Chem. 253, 8968–8971 (1978).

    CAS  PubMed  Google Scholar 

  74. Hofmann, F. Apparent constants for the interaction of regulatory and catalytic subunit of cAMP-dependent protein kinase I and II. J. Biol. Chem. 255, 1559–1564 (1980).

    CAS  PubMed  Google Scholar 

  75. Anand, G. S., Hughes, C. A., Jones, J. M., Taylor, S. S. & Komives, E. A. Amide H/2H exchange reveals communication between the cAMP and catalytic subunit-binding sites in the R(I)α subunit of protein kinase A. J. Mol. Biol. 323, 377–386 (2002).

    Article  CAS  PubMed  Google Scholar 

  76. Hamuro, Y. et al. Dynamics of cAPK type IIβ activation revealed by enhanced amide H/2H exchange mass spectrometry (DXMS). J. Mol. Biol. 327, 1065–1076 (2003).

    Article  CAS  PubMed  Google Scholar 

  77. Zhao, J., Hoye, E., Boylan, S., Walsh, D. A. & Trewhella, J. Quaternary structures of a catalytic subunit-regulatory subunit dimeric complex and the holoenzyme of the cAMP-dependent protein kinase by neutron contrast variation. J. Biol. Chem. 273, 30448–30459 (1998).

    Article  CAS  PubMed  Google Scholar 

  78. Vigil, D., Blumenthal, D. K., Taylor, S. S. & Trewhella, J. The conformationally dynamic C helix of the RIα subunit of protein kinase A mediates isoform-specific domain reorganization upon C subunit binding. J. Biol. Chem. 280, 35521–35527 (2005).

    Article  CAS  PubMed  Google Scholar 

  79. Wolfe, L., Francis, S. H. & Corbin, J. D. Properties of a cGMP-dependent monomeric protein kinase from bovine aorta. J. Biol. Chem. 264, 4157–4162 (1989).

    CAS  PubMed  Google Scholar 

  80. Aggarwal, S. K. & MacKinnon, R. Contribution of the S4 segment to gating charge in the Shaker K+ channel. Neuron 16, 1169–1177 (1996).

    Article  CAS  PubMed  Google Scholar 

  81. Alioua, A. et al. The large conductance, voltage-dependent, and calcium-sensitive K+ channel, Hslo, is a target of cGMP-dependent protein kinase phosphorylation in vivo. J. Biol. Chem. 273, 32950–32956 (1998).

    Article  CAS  PubMed  Google Scholar 

  82. Jiang, Y. et al. X-ray structure of a voltage-dependent K+ channel. Nature 423, 33–41 (2003).

    Article  CAS  PubMed  Google Scholar 

  83. Kuo, A. et al. Crystal structure of the potassium channel KirBac1.1 in the closed state. Science 300, 1922–1926 (2003).

    Article  CAS  Google Scholar 

  84. Jiang, Y. et al. The open pore conformation of potassium channels. Nature 417, 523–526 (2002).

    Article  CAS  Google Scholar 

  85. Craven, K. B. & Zagotta, W. N. Salt bridges and gating in the COOH-terminal region of HCN2 and CNGA1 channels. J. Gen. Physiol. 124, 663–677 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Johnson, J. P. Jr. & Zagotta, W. N. The carboxyl-terminal region of cyclic nucleotide-modulated channels is a gating ring, not a permeation path. Proc. Natl Acad. Sci. USA 102, 2742–2747 (2005).

    Article  CAS  PubMed  Google Scholar 

  87. Wainger, B. J., De Gennaro, M., Santoro, B., Siegelbaum, S. A. & Tibbs, G. R. Molecular mechanism of cAMP modulation of HCN pacemaker channels. Nature 411, 805–810 (2001).

    Article  CAS  PubMed  Google Scholar 

  88. de Rooij, J. et al. Mechanism of regulation of the Epac family of cAMP-dependent RapGEFs. J. Biol. Chem. 275, 20829–20836 (2000).

    Article  CAS  PubMed  Google Scholar 

  89. Herrmann, C. Ras-effector interactions: after one decade. Curr. Opin. Struct. Biol. 13, 122–129 (2003).

    Article  CAS  PubMed  Google Scholar 

  90. Coccetti, P., Mauri, I., Alberghina, L., Martegani, E. & Parmeggiani, A. The minimal active domain of the mouse ras exchange factor CDC25Mm. Biochem. Biophys. Res. Commun. 206, 253–259 (1995).

    Article  CAS  PubMed  Google Scholar 

  91. Boriack-Sjodin, P. A., Margarit, S. M., Bar-Sagi, D. & Kuriyan, J. The structural basis of the activation of Ras by Sos. Nature 394, 337–343 (1998).

    Article  CAS  PubMed  Google Scholar 

  92. Botelho, L. H., Rothermel, J. D., Coombs, R. V. & Jastorff, B. cAMP analog antagonists of cAMP action. Methods Enzymol. 159, 159–172 (1988).

    Article  CAS  PubMed  Google Scholar 

  93. Wu, J., Jones, J. M., Xuong, N. H., Ten Eyck, L. F. & Taylor, S. S. Crystal structures of RIα subunit of cyclic adenosine 5′-monophosphate (cAMP)-dependent protein kinase complexed with (Rp)-adenosine 3′,5′-cyclic monophosphothioate and (Sp)-adenosine 3′,5′-cyclic monophosphothioate, the phosphothioate analogues of cAMP. Biochemistry 43, 6620–6629 (2004).

    Article  CAS  PubMed  Google Scholar 

  94. Kraulis, P. J. Molscript — a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  95. Merritt, E. A. & Murphy, M. E. P. Rasert3D version-2.0 — a program for photorealistic molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 50, 869–873 (1994).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank F. Zwartkruis and B. Burgering for stimulating discussions. H.R. is supported by the Chemical Sciences of the Netherlands Organization for Scientific Research (NWO-CW).

Author information

Authors and Affiliations

  1. Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands

    Holger Rehmann & Johannes L. Bos

  2. Max-Planck Institut fr Molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund, D-44227, Germany

    Alfred Wittinghofer

Authors
  1. Holger Rehmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alfred Wittinghofer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Johannes L. Bos
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Holger Rehmann.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information S1 (movie)

Cyclic-nucleotide-induced conformational changes in cyclic-nucleotide-binding domains. A schematic representation of a cyclic-nucleotide-binding domain is shown. The central core of the domain (the β- sandwich) is depicted in yellow and grey and being barrel shaped. The N-terminal helical bundle, the hinge and the lid are represented as orange helices and labelled correspondingly. The movie shows an animation of the conformational changes that occur in cyclic-nucleotide-binding domains following the binding of cyclic nucleotide (see also FIG. 4). The cyclic nucleotide (shown in red with the phosphate group (P) coloured blue) enters the binding site, and the phosphate-binding cassette (PBC) undergoes rearrangements to allow it to interact with the phosphate sugar moiety of the cyclic nucleotide (red dotted lines represent hydrogen bonds). As a result, the Leu residue at position six in the PBC, which is shown in a red stick representation, is repositioned and its movement leaves a space that allows a conserved Phe or Tyr residue (a Phe is shown here in orange) in the hinge to move closer to the core of the domain (the β-sandwich). A rearrangement of the N-terminal helical bundle is associated with the movement of the hinge. When the hinge adopts its final conformation, it positions the lid over the cyclic nucleotide and the conformation of the lid is stabilized by mainly hydrophobic interactions with the base of the nucleotide (black and red striped lines represent hydrophobic interactions). (MOV 1960 kb)

Related links

Related links

DATABASES

Protein Data Bank

1BKD

1U7E

1U12

1VP6

1VPC

2BYV

Glossary

Glycogen

A polysaccharide that is composed of chains of glucose molecules. Glycogen is a storage form of glucose in the body.

Heterotrimeric G-protein

Comprises an α-, β- and γ-subunit. The α-subunit binds GDP or GTP. Exchange of GDP to GTP is stimulated by agonist-stimulated transmembrane receptors and causes dissociation into the α-subunit and a βγ-complex, which control downstream signalling cascades.

Natriuresis

The excretion of an excessively large amount of Na+ ions in the urine. The consequence of natriuresis is that extracellular liquid volume and, therefore, blood pressure are reduced.

Atrial natriuretic peptide

(ANP). A small protein that is mainly released by endocrine heart cells following distension of the right atrium. ANP is generated by the cleavage of its precursor protein.

GAF domain

Named GAF because it is found in cGMP-specific and cGMP-stimulated phosphodiesterases, Anabaena adenylyl cyclases and Escherichia coli FhlA proteins. When present in phosphodiesterases or adenylyl cyclases, this domain usually binds cGMP and cAMP. In some plant and cyanobacterial phytochromes, a GAF domain is the site of chromophore attachment.

HCN channel

(Hyperpolarization-activated, cyclic-nucleotide-modulated channel). A cationic ion channel that is regulated mainly by the membrane potential. Cyclic nucleotide binding modifies the activation characteristics of the channel by shifting the threshold membrane potential needed for channel opening.

Lac operon

A group of three genes that are involved in the metabolism of lactose. The expression of these genes is controlled by a single promoter that is activated by catabolite activator protein (CAP).

PKA type II (and type I)

In higher organisms, four different regulatory subunits of PKA, namely type Iα, type Iβ, type IIα and type IIβ, exist. PKAs can be stimulated by cAMP and can then phosphorylate downstream targets.

Leucine zipper

A specialized coiled-coil motif that can induce the dimerization of α-helices. The helices are held together by hydrophobic interactions between the Leu residues that are located on one side of the amphipathic helices.

Pseudo-substrate sequence

A sequence that resembles the consensus sequence of a kinase, with the exception that the residue that normally accepts the γ-phosphate group is replaced by an Ala residue. The pseudo-substrate sequence binds to the catalytic cleft of the kinase domain and therefore traps the catalytic subunit in an unproductive complex.

Deuterium-exchange method

A technique to measure the accessibility of residues to solvent. Time-limited exposure of a protein to deuterium oxide (heavy water) results in the exchange of solvent-exposed protons by deuterium, which can be analysed by mass spectrometry.

CNG channel

(Cyclic-nucleotide-gated channel). The binding of cyclic nucleotides to this cationic ion channel directly controls the probability of the channel being open. Membrane potential has almost no effect on the regulation of CNG channels.

Gating current

The current that is measured during channel opening and that is independent of the ion flux across the membrane. The current originates from the movement of charged amino-acid residues due to the conformational changes that occur in the channel during opening.

DEP domain

(Dishevelled, Egl-10, Pleckstrin domain). A 90amino-acid domain that is thought to be involved in the membrane localization of the protein in which the domain is present, although the exact targeting mechanism is unknown.

REM domain

(Ras-exchanger-motif domain). A domain that is present in guanine nucleotide-exchange factors for small G-proteins of the Ras family. They mainly provide structural shielding and stabilizing roles.

RA domain

(Ras-association domain; RalGDS/AF6 domain). A domain with a ubiquitin-like fold that is found in effectors of G-proteins of the Ras superfamily. RA domains interact specifically with the GTP-bound conformation of these G-proteins.

Ras

A small G-protein that is part of the Ras superfamily of small G proteins. Members of this family are structurally highly similar and are activated by guanine nucleotide-exchange factors. Ras has an important role in cell-growth control and is mutated in 15% of all human tumours.

Sos

(Son-of-sevenless). Sos is a guanine nucleotide-exchange factor for the Rap-related G-protein Ras.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rehmann, H., Wittinghofer, A. & Bos, J. Capturing cyclic nucleotides in action: snapshots from crystallographic studies. Nat Rev Mol Cell Biol 8, 63–73 (2007). https://doi.org/10.1038/nrm2082

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm2082

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