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.

Structural basis of BMP signalling inhibition by the cystine knot protein Noggin

Abstract

The interplay between bone morphogenetic proteins (BMPs) and their antagonists governs developmental and cellular processes as diverse as establishment of the embryonic dorsal–ventral axis, induction of neural tissue, formation of joints in the skeletal system and neurogenesis in the adult brain. So far, the three-dimensional structures of BMP antagonists and the structural basis for inactivation have remained unknown. Here we report the crystal structure of the antagonist Noggin bound to BMP-7, which shows that Noggin inhibits BMP signalling by blocking the molecular interfaces of the binding epitopes for both type I and type II receptors. The BMP-7-binding affinity of site-specific variants of Noggin is correlated with alterations in bone formation and apoptosis in chick limb development, showing that Noggin functions by sequestering its ligand in an inactive complex. The scaffold of Noggin contains a cystine (the oxidized form of cysteine) knot topology similar to that of BMPs; thus, ligand and antagonist seem to have evolved from a common ancestral gene.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Sequence alignment of Noggin, DAN family antagonists and BMPs.
Figure 2: Structure of the Noggin–BMP-7 complex.
Figure 3: The Noggin monomer contains a ‘growth factor’ cystine knot scaffold.
Figure 4: Structural basis for inhibition of receptor binding by Noggin.
Figure 5: Binding affinity of Noggin proteins for BMP-7.
Figure 6: In vivo effects of Noggin on BMP-induced chondrogenesis and apoptosis.

References

  1. Massague, J. TGF-β signal transduction. Annu. Rev. Biochem. 67, 753–791 (1998)

    Article  CAS  Google Scholar 

  2. Hogan, B. L. Bone morphogenetic proteins: multifunctional regulators of vertebrate development. Genes Dev. 10, 1580–1594 (1996)

    Article  CAS  Google Scholar 

  3. Smith, W. C. TGFβ inhibitors. Trends Genet. 15, 3–5 (1999)

    Article  CAS  Google Scholar 

  4. Urist, M. R. Bone: formation by autoinduction. Science 150, 893–899 (1965)

    Article  ADS  CAS  Google Scholar 

  5. Smith, W. C. & Harland, R. M. Expression cloning of noggin, a new dorsalizing factor localized to the Spemann organizer in Xenopus embryos. Cell 70, 829–840 (1992)

    Article  CAS  Google Scholar 

  6. Hsu, D. R., Economides, A. N., Wang, X., Eimon, P. M. & Harland, R. M. The Xenopus dorsalizing factor Gremlin identifies a novel family of secreted proteins that antagonize BMP activities. Mol. Cell 1, 673–683 (1998)

    Article  CAS  Google Scholar 

  7. Piccolo, S., Sasai, Y., Lu, B. & De Robertis, E. M. Dorsoventral patterning in Xenopus: inhibition of ventral signals by direct binding of chordin to BMP-4. Cell 86, 589–598 (1996)

    Article  CAS  Google Scholar 

  8. Zimmerman, L. B., De Jesus-Escobar, J. M. & Harland, R. M. The Spemann organizer signal noggin binds and inactivates bone morphogenetic protein 4. Cell 86, 599–606 (1996)

    Article  CAS  Google Scholar 

  9. Brunet, L. J., McMahon, J. A., McMahon, A. P. & Harland, R. M. Noggin, cartilage morphogenesis, and joint formation in the mammalian skeleton. Science 280, 1455–1457 (1998)

    Article  ADS  CAS  Google Scholar 

  10. Gong, Y. et al. Heterozygous mutations in the gene encoding noggin affect human joint morphogenesis. Nature Genet. 21, 302–304 (1999)

    Article  CAS  Google Scholar 

  11. Dixon, M. E., Armstrong, P., Stevens, D. B. & Bamshad, M. Identical mutations in NOG can cause either tarsal/carpal coalition syndrome or proximal symphalangism. Genet. Med. 3, 349–353 (2001)

    Article  CAS  Google Scholar 

  12. Takahashi, T. et al. Mutations of the NOG gene in individuals with proximal symphalangism and multiple synostosis syndrome. Clin. Genet. 60, 447–451 (2001)

    Article  CAS  Google Scholar 

  13. Lim, D. A. et al. Noggin antagonizes BMP signalling to create a niche for adult neurogenesis. Neuron 28, 713–726 (2000)

    Article  CAS  Google Scholar 

  14. Ogawa, K. et al. Induction of a noggin-like gene by ectopic DV interaction during planarian regeneration. Dev. Biol. 250, 59–70 (2002)

    Article  CAS  Google Scholar 

  15. Economides, A. N., Stahl, N. E., & Harland, R. M. Modified noggin polypeptide and compositions. US Patent 6,075,007 (2000).

  16. Paine-Saunders, S., Viviano, B. L., Economides, A. N. & Saunders, S. Heparan sulfate proteoglycans retain Noggin at the cell surface: a potential mechanism for shaping bone morphogenetic protein gradients. J. Biol. Chem. 277, 2089–2096 (2002)

    Article  CAS  Google Scholar 

  17. Groppe, J. et al. Biochemical and biophysical characterization of refolded Drosophila DPP, a homolog of bone morphogenetic proteins 2 and 4. J. Biol. Chem. 273, 29052–29065 (1998)

    Article  CAS  Google Scholar 

  18. Dauter, Z., Dauter, M. & Rajashankar, K. R. Novel approach to phasing proteins: derivatization by short cryo- soaking with halides. Acta Crystallogr. D 56, 232–237 (2000)

    Article  CAS  Google Scholar 

  19. Griffith, D. L., Keck, P. C., Sampath, T. K., Rueger, D. C. & Carlson, W. D. Three-dimensional structure of recombinant human osteogenic protein 1: structural paradigm for the transforming growth factor β superfamily. Proc. Natl Acad. Sci. USA 93, 878–883 (1996)

    Article  ADS  CAS  Google Scholar 

  20. Vitt, U. A., Hsu, S. Y. & Hsueh, A. J. Evolution and classification of cystine knot-containing hormones and related extracellular signaling molecules. Mol. Endocrinol. 15, 681–694 (2001)

    Article  CAS  Google Scholar 

  21. Kirsch, T., Nickel, J. & Sebald, W. BMP-2 antagonists emerge from alterations in the low-affinity binding epitope for receptor BMPR-II. EMBO J. 19, 3314–3324 (2000)

    Article  CAS  Google Scholar 

  22. Kirsch, T., Sebald, W. & Dreyer, M. K. Crystal structure of the BMP-2–BRIA ectodomain complex. Nature Struct. Biol. 7, 492–496 (2000)

    Article  CAS  Google Scholar 

  23. Stanley, E. et al. DAN is a secreted glycoprotein related to Xenopus cerberus. Mech. Dev. 77, 173–184 (1998)

    Article  CAS  Google Scholar 

  24. Isaacs, N. W. Cystine knots. Curr. Opin. Struct. Biol. 5, 391–395 (1995)

    Article  CAS  Google Scholar 

  25. Sun, P. D. & Davies, D. R. The cystine-knot growth-factor superfamily. Annu. Rev. Biophys. Biomol. Struct. 24, 269–291 (1995)

    Article  CAS  Google Scholar 

  26. Hatta, T. et al. Identification of the ligand-binding site of the BMP type IA receptor for BMP-4. Biopolymers 55, 399–406 (2000)

    Article  CAS  Google Scholar 

  27. Capdevila, J. & Johnson, R. L. Endogenous and ectopic expression of noggin suggests a conserved mechanism for regulation of BMP function during limb and somite patterning. Dev. Biol. 197, 205–217 (1998)

    Article  CAS  Google Scholar 

  28. Merino, R. et al. Morphogenesis of digits in the avian limb is controlled by FGFs, TGFβs, and noggin through BMP signaling. Dev. Biol. 200, 35–45 (1998)

    Article  CAS  Google Scholar 

  29. Capdevila, J., Tsukui, T., Rodriquez Esteban, C., Zappavigna, V. & Izpisua Belmonte, J. C. Control of vertebrate limb outgrowth by the proximal factor Meis2 and distal antagonism of BMPs by Gremlin. Mol. Cell 4, 839–849 (1999)

    Article  CAS  Google Scholar 

  30. Merino, R. et al. The BMP antagonist Gremlin regulates outgrowth, chondrogenesis and programmed cell death in the developing limb. Development 126, 5515–5522 (1999)

    CAS  PubMed  Google Scholar 

  31. Zuniga, A., Haramis, A. P., McMahon, A. P. & Zeller, R. Signal relay by BMP antagonism controls the SHH/FGF4 feedback loop in vertebrate limb buds. Nature 401, 598–602 (1999)

    Article  ADS  CAS  Google Scholar 

  32. Iemura, S. et al. Direct binding of follistatin to a complex of bone-morphogenetic protein and its receptor inhibits ventral and epidermal cell fates in early Xenopus embryo. Proc. Natl Acad. Sci. USA 95, 9337–9342 (1998)

    Article  ADS  CAS  Google Scholar 

  33. Francis-West, P. H., Parish, J., Lee, K. & Archer, C. W. BMP/GDF-signalling interactions during synovial joint development. Cell Tissue Res. 296, 111–119 (1999)

    Article  CAS  Google Scholar 

  34. Duprez, D. et al. Overexpression of BMP-2 and BMP-4 alters the size and shape of developing skeletal elements in the chick limb. Mech. Dev. 57, 145–157 (1996)

    Article  CAS  Google Scholar 

  35. Macias, D. et al. Role of BMP-2 and OP-1 (BMP-7) in programmed cell death and skeletogenesis during chick limb development. Development 124, 1109–1117 (1997)

    CAS  PubMed  Google Scholar 

  36. Enomoto-Iwamoto, M. et al. Bone morphogenetic protein signaling is required for maintenance of differentiated phenotype, control of proliferation, and hypertrophy in chondrocytes. J. Cell Biol. 140, 409–418 (1998)

    Article  CAS  Google Scholar 

  37. Yokouchi, Y. et al. BMP-2/-4 mediate programmed cell death in chicken limb buds. Development 122, 3725–3734 (1996)

    CAS  PubMed  Google Scholar 

  38. Zou, H. & Niswander, L. Requirement for BMP signaling in interdigital apoptosis and scale formation. Science 272, 738–741 (1996)

    Article  ADS  CAS  Google Scholar 

  39. Gañan, Y., Macias, D., Duterque-Coquillaud, M., Ros, M. A. & Hurle, J. M. Role of TGFβs and BMPs as signals controlling the position of the digits and the areas of interdigital cell death in the developing chick limb autopod. Development 122, 2349–2357 (1996)

    PubMed  Google Scholar 

  40. Healy, C., Uwanogho, D. & Sharpe, P. T. Regulation and role of Sox9 in cartilage formation. Dev. Dyn. 215, 69–78 (1999)

    Article  CAS  Google Scholar 

  41. Marcelino, J. et al. Human disease-causing NOG missense mutations: effects on noggin secretion, dimer formation, and bone morphogenetic protein binding. Proc. Natl Acad. Sci. USA 98, 11353–11358 (2001)

    Article  ADS  CAS  Google Scholar 

  42. Mangino, M., Flex, E., Digilio, M. C., Giannotti, A. & Dallapiccola, B. Identification of a novel NOG gene mutation (P35S) in an Italian family with symphalangism. Hum. Mutat. 19, 308 (2002)

    Article  CAS  Google Scholar 

  43. Sampath, T. K. et al. Recombinant human osteogenic protein-1 (hOP-1) induces new bone formation in vivo with a specific activity comparable with natural bovine osteogenic protein and stimulates osteoblast proliferation and differentiation in vitro. J. Biol. Chem. 267, 20352–20362 (1992)

    CAS  PubMed  Google Scholar 

  44. Valenzuela, D. M. et al. Identification of mammalian noggin and its expression in the adult nervous system. J. Neurosci. 15, 6077–6084 (1995)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  46. Terwilliger, T. C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849–861 (1999)

    Article  CAS  Google Scholar 

  47. Collaborative Computational Project Number 4 The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

    Article  Google Scholar 

  48. Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994)

    Article  CAS  Google Scholar 

  49. Russell, R. B. & Barton, G. J. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins Struct. Funct. Genet. 14, 309–323 (1992)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Curis for BMP-7; Regeneron Pharmaceuticals for Noggin; K. Baban for technical assistance; M. Austin for aid with crystal/cryo-optimization; G. Louie for phasing advice; and the staff at SSRL for help with data collection. The SSRL Structural Molecular Biology Program is supported by the Department of Energy and the NIH. J. Groppe is grateful to K. Kirschner and T. Kiefhaber for their initial support. J. Greenwald acknowledges support from a National Cancer Institute Training Grant. This work was supported by grants from the Swiss National Science Foundation and the Kantons Basel (M.A.), BioCell, National Science Foundation, the G. Harold and Leila Y. Mathers Charitable Foundation, and the Fundacao Calouste Gulbenkian and Fundacao para Ciencia e Technologia (J.R.L., J.C.I.B.), and the National Institutes of Health (S.C., W.W.V.).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Senyon Choe.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Groppe, J., Greenwald, J., Wiater, E. et al. Structural basis of BMP signalling inhibition by the cystine knot protein Noggin. Nature 420, 636–642 (2002). https://doi.org/10.1038/nature01245

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature01245

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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