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 the carboxy-terminal LIM domain from the cysteine rich protein CRP

Nature Structural Biology volume 1, pages 388–398 (1994)Cite this article

Abstract

The three dimensional solution structure of the carboxy terminal LIM domain of the avian Cysteine Rich Protein (CRP) has been determined by nuclear magnetic resonance spectroscopy. The domain contains two zinc atoms bound independently in CCHC (C=Cys, H=His) and CCCC modules. Both modules contain two orthogonally-arranged antiparallel β-sheets, and the CCCC module contains an α-helix at its C terminus. The modules pack due to hydrophobic interactions forming a novel global fold. The structure of the C-terminal CCCC module is essentially identical to that observed for the DNA-interactive CCCC modules of the GATA-1 and steroid hormone receptor DNA binding domains, raising the possibility that the LIM motif may have a DNA binding function.

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

Similar content being viewed by others

References

  1. Karlsson, O., Thor, S., Norberg, T., Ohlsson, H. & Edlund, T. Insulin gene enhancer binding protein Isl-1 is a member of a novel class of proteins containing both a homeo- and a cys-his domain. Nature 344, 879–882 (1990).

    Article  CAS  Google Scholar 

  2. Freyd, G., Kim, S.K. & Horvitz, R. Novel cysteine-rich motif and homeodomain in the product of the Caenorhabditis elegans cell lineage gene lin-11 . Nature 344, 876–879 (1990).

    Article  CAS  Google Scholar 

  3. Xu, Y., Baldassare, M., Fisher, P., Rathbun, G., Oltz, E.M., Yancopoulos, G.D., Jessell, T.M. & Alt, F.W. LH-2: a LIM/homeodomain gene expressed in developing lymphocytes and neural cells. Proc. natn. Acad. Sci. U.S.A. 90, 227–231 (1993).

    Article  CAS  Google Scholar 

  4. Bourgouin, C., Lundgren, S.E. & Thomas, J.B. Apterous is a drosophila LIM domain gene required for the development of a subset of embryonic muscles. Neuron 9, 549–561 (1992).

    Article  CAS  Google Scholar 

  5. Cohen, B., McGuffin, M.E., Pfeifle, C., Segal, D. & Cohen, S.M. Apterous, a gene required for imaginal disc development in Drosophila encodes a member of the LIM family of developmental regulatory proteins. Genes Devel. 6, 715–729 (1992).

    Article  CAS  Google Scholar 

  6. Taira, M., Jamrich, M., Good, P.J. & Dawid, I.B. The LIM domain-containing homeo box gene Xlim-1 is expressed specifically in the organizer region of Xenopus gastrula embryos. Genes Devel. 6, 356–366 (1992).

    Article  CAS  Google Scholar 

  7. Boehm, T., Greenberg, J.M., Buluwela, L., Lavenir, I., Forster, A. & Rabbitts, T.H. An unusual structure of a putative T cell oncogene which allows production of similar proteins from distinct mRNAs. EMBO J. 9, 857–868 (1990).

    Article  CAS  Google Scholar 

  8. Birkenmeier, E.H., & Gordon, J.I. Developmental regulation of a gene that encodes a cysteine-rich intestinal protein and maps near the murine immonoglobulin heavy chain locus. Proc. natn. Acad. Sci. USA 83, 2516–2520 (1986).

    Article  CAS  Google Scholar 

  9. Sadler, I., Crawford, A.W., Michelsen, J.W. & Beckerle, M.C. Zyxin and cCRP: two interactive LIM domain proteins associated with the cytoskeleton. J. cell. Biol. 119, 1573–1587 (1992).

    Article  CAS  Google Scholar 

  10. Liebhaber, S.A., Emery, J.G., Urbanek, M., Wang, X. & Cook, N.E. Characterization of a human cDNA encoding a widely expressed and highly conserved cysteine-rich protein with an unusual zinc-finger motif. Nucl. Acids Res. 18, 3871–3879 (1990).

    Article  CAS  Google Scholar 

  11. Crawford, A.W., Pino, J.D. & Beckerle, M.C. Biochemical and molecular characterization of the chicken cysteine-rich protein, a developmentally regulated LIM-domain protein that is associated with the actin cytoskeleton. J. cell. Biol. 124, 117–127 (1994).

    Article  CAS  Google Scholar 

  12. McGuire, A.E. et al. The t (11;14) p15;q11) in a T-cell acute lymphoblastic leukemia cell line activates multiple transcripts, including ttg-1, a gene encoding a potential zinc finger protein. Molec. cell. Biol. 9, 2124–2532 (1989).

    Article  CAS  Google Scholar 

  13. Wang, X., Lee, G., Liebhaber, S.A. & Cooke, N.E. Human cystein-rich protein. A member of the LIM/double-finger family displaying coordinate serum induction with c-myc . J. biol. Chem. 267, 9176–9184 (1992).

    CAS  PubMed  Google Scholar 

  14. Weiskirchen, R. & Bister, K. Suppression in transformed avian fibroblasts of a gene (crp) encoding a cysteine-rich protein containing LIM domains. Oncogene 8, 2317–2324 (1993).

    CAS  PubMed  Google Scholar 

  15. Kosa, J.L. et al. Common metal ion coordination in LIM domain proteins. Biochemistry 33, 468–477 (1994).

    Article  CAS  Google Scholar 

  16. Michelsen, J.W., Schmeichel, K.L., Beckerle, M.C. & Winge, D.R. The LIM motif defines a specific zinc-binding protein domain. Proc. natn. Acad. Sci. U.S.A. 90, 4404–4408 (1993).

    Article  CAS  Google Scholar 

  17. Archer, V.E.V. et al. Cysteine-rich LIM domains of LIM-homeodomain and LIM-only proteins contain zinc but not iron. Proc. natn. Acad. Sci. U.S.A. 91, 316–320 (1994).

    Article  CAS  Google Scholar 

  18. Wüthrich, K. NMR of Proteins and Nucleic Acids (John Wiley, New York, 1986).

    Book  Google Scholar 

  19. Mueller, L. Sensitivity enhanced detection of weak nuclei using heteronuclear multiple quantum coherence. J. Am. chem. Soc. 101, 4481–4484 (1979).

    Article  CAS  Google Scholar 

  20. Bax, A., Griffey, R.H. & Hawkins, B.L. Correlation of proton and nitrogen-15 chemical shifts by multiple quantum NMR. J. Magn. Reson. 55, 301–315 (1983).

    CAS  Google Scholar 

  21. Adman, E., Watenpaugh, E.D. & Jensen, L.H. NH—S hydrogen bonds in Peptococcus aerogenes ferredoxin, Clostridium pasteurianum rubredoxin, and Chromatium high potential iron protein. Proc. natn. Acad. Sci. U.S.A. 72, 4854 (1975).

    Article  CAS  Google Scholar 

  22. South, T.L., Blake, P.R., Hare, D.R. & Summers, M.F. C-terminal retroviral-type zinc finger domain from the HIV-1 nucleocapsid protein is structurally similar to the N-terminal zinc finger domain Biochemistry 30, 6342–6349 (1991).

    Article  CAS  Google Scholar 

  23. Summers, M.F., South, T.L., Kim, B. & Hare, D.R. Structure of an HIV-1 zinc fingerlike domain via a new NMR-based distance geometry approach. Biochemistry 29, 329–340 (1990).

    Article  CAS  Google Scholar 

  24. Blake, P.R. & Summers, M.F. Probing the unusually similar metal coordination sites of retroviral zinc fingers and iron-sulfur proteins by nuclear magnetic resonance Adv. biophys. Chem. (in the press).

  25. Fourmy, D., Dardel, F. & Blanquet, S. Methionyl-tRNA synthetase zinc binding domain Three-dimensional structure and homology with rubredoxin and gag retroviral proteins. J. molec. Biol. 231, 1078–1089 (1993).

    Article  CAS  Google Scholar 

  26. Kochoyan, M., Havel, T.F., Nguyen, D.T., Dahl, C.E., Keutmann, H.T. & Weiss, M.A. Alternating zinc fingers in the human male associated protein ZFY: 2D NMR structure of an even-finger and implications for “jumping-linker” DNA recognition. Biochemistry 30, 3371–3386 (1991).

    Article  CAS  Google Scholar 

  27. Kochoyan, M., Keutmann, H.G. & Weiss, M.A. Alternating zinc fingers in the human male associated protein ZFY: Refinement of the NMR structure of an even finger by selective deuterium labeling and implications for DNA recognition. Biochemistry 30, 7063–7072 (1991).

    Article  CAS  Google Scholar 

  28. Lee, M.S., Gippert, G.P., Soman, D.A., Case, D.A. & Wright, P.E. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 254, 635 (1989).

    Article  Google Scholar 

  29. Hoffman, R.C., Xu, R., Klevit, R.E. & Herriott, J.R. A simple method for the refinement of models derived from NMR data demonstrated on a zinc-finger domain from yeast ADR1. J. magn. Reson. 102, 61–72 (1993).

    Article  CAS  Google Scholar 

  30. Pavletich, N.P. & Pabo, C.O. Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å. Science 252, 809–817 (1991).

    Article  CAS  Google Scholar 

  31. Lee, M.S., Kliewer, S.A., Provencal, J., Wright, P.E. & Evans, R.M. Structure of the retinoid X receptor alpha DNA binding domain: A helix required for homodimeric DNA binding. Science 260, 1117 (1993).

    Article  CAS  Google Scholar 

  32. Luisi, B.F. et al. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature 352, 497–505 (1991).

    Article  CAS  Google Scholar 

  33. Knegtel, R.M.A. et al. The solution structure of the human retinoic acid receptor-β DNA-binding domain. J. biomolec. NMR 3, 1–17 (1993).

    Article  CAS  Google Scholar 

  34. Schwabe, J.W.R., Neuhaus, D. & Rhodes, D. Solution structure of the DNA-binding domain of the oestrogen receptor. Nature 348, 458–461 (1990).

    Article  CAS  Google Scholar 

  35. Hard, T. et al. Solution structure of the glucocorticoid receptor DNA-binding domain. Science 249, 157–160 (1990).

    Article  CAS  Google Scholar 

  36. Baumann, H. et al. Refined solution structure of the glucocorticoid receptor DNA-binding domain. Biochemistry 32, 13463–13471 (1994).

    Article  Google Scholar 

  37. Kraulis, P.J., Raine, A.R.C., Gadhavi, P.L. & Laue, E.D. Structure of the DNA-binding domain of zinc GAL4. Nature 356, 448–450 (1992).

    Article  CAS  Google Scholar 

  38. Baleja, J.D., Marmorstein, R., Harrison, S.C. & Wagner, G. Solution structure of the DNA-binding domain of Cd2-GAL4 from S. cerevisiae . Nature 356, 450–453 (1992).

    Article  CAS  Google Scholar 

  39. Marmorstein, R., Carey, M., Ptashne, M. & Harrison, S.C. DNA recognition by GAL4: structure of a protein–DNA complex. Nature 356, 408–414 (1992).

    Article  CAS  Google Scholar 

  40. Omichinski, J.G. et al. NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science 261, 438–446 (1993).

    Article  CAS  Google Scholar 

  41. Blake, P.B. et al. Heteronuclear magnetic resonance studies of Zn, 113Cd and 199Hg substituted P. furiosus rubredoxin: Implications for biological electron transfer. New J. Chem. 18, 387–395 (1994).

    CAS  Google Scholar 

  42. Blake, P.R., Park, J.B., Adams, M.W.W. & Summers, M.F. Novel observation of NH-S hydrogen bond mediated scalar coupling in 113Cd-substituted rubredoxin from the marine hyperthermophile, Pyrococcus furiosus . J. Am. chem. Soc. 114, 4931–4933 (1992).

    Article  CAS  Google Scholar 

  43. Blake, P.R. et al. Quantitative measurement of small through-hydrogen-bond and ‘through-space’ 1H-113Cd and 1H-199Hg J couplings in metal-substituted rubredoxin from Pyrococcus furiosus . J. biomolec. NMR 2, 527–533 (1992).

    Article  CAS  Google Scholar 

  44. Clore, G.M., Gronenborn, A.M., Nilges, M. & Ryan, C.A. Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics. Biochemistry 26, 8012–8023 (1987).

    Article  CAS  Google Scholar 

  45. Blake, P.R. et al. Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus . Prot. Sci. 1, 1508–1521 (1992).

    Article  CAS  Google Scholar 

  46. Clore, G.M. & Gronenborn, A.M. Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy. Science 252, 1390–1399 (1991).

    Article  CAS  Google Scholar 

  47. Chakrabarti, P. Geometry of interaction of metal ions with histidine residues in protein structures. Prot. Engng. 4, 57–63 (1990).

    Article  CAS  Google Scholar 

  48. Li, Y. & Tsai, M.-D. Phospholipase A2 engineering. 10. The aspartate-histidine catalytic diad also plays an important structural role. J. Am. chem. Soc. 115, 8523–8526 (1993).

    Article  CAS  Google Scholar 

  49. Everett, R.D. et al. A novel arrangement of zinc-binding residues and secondary structure in the C3HC4 motif of an alpha herpes virus protein family. J. molec. Biol. 234, 1038–1047 (1993).

    Article  CAS  Google Scholar 

  50. Barlow, P.N., Luisi, B., Milner, A., Elliott, M. & Everett, R. Structure of the C3HC4 domain by 1H-nuclear magnetic resonance spectroscopy. J. molec. Biol. 237, 201–211 (1994).

    Article  CAS  Google Scholar 

  51. Griesinger, C., Otting, G., Wüthrich, K. & Ernst, R.R. Clean TOCSY for 1H spin system identification in macromolecules. J. Am. chem. Soc. 110, 7870–7872 (1988).

    Article  CAS  Google Scholar 

  52. Hore, P.J. Solvent suppression in Fourier transform nuclear magnetic resonance. J. magn. Reson. 55, 283–300 (1983).

    CAS  Google Scholar 

  53. Brown, S.C., Weber, P.L. & Mueller, L. Toward complete 1H NMR spectra in proteins. J. magn. Reson. 77, 166–169 (1988).

    CAS  Google Scholar 

  54. Blake, P.R. et al. Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR. Biochemistry 30, 10885–10895 (1991).

    Article  CAS  Google Scholar 

  55. Pauly, J., LeRoux, P., Mishimura, B. & Macovski, A. IEEE Trans. Med. Imaging 53, (1991).

  56. Shinnar, M., Eleff, S., Subramanian, H. & Leigh, J.S. The synthesis of pulse sequences yielding arbitrary magnetization vectors. Magn. Reson. Med. 12, 74–80 (1989).

    Article  CAS  Google Scholar 

  57. 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 

  58. Bacon, D.J. & Anderson, W.F. A fast algorithm for rendering space-filling molecule pictures. J. molec. Graphics 6, 219–220 (1988).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. The Howard Hughes Medical Institute and the Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland, 21228, USA

    Gabriela C. Pérez-Alvarado, Colleen Miles & Michael F. Summers

  2. Department of Biology, University of Utah, Salt Lake City, Utah, 84132, USA

    James W. Michelsen, Heather A. Louis & Mary C. Beckerle

  3. Departments of Medicine and Biochemistry, University of Utah, Salt Lake City, Utah, 84132, USA

    Dennis R. Winge

Authors
  1. Gabriela C. Pérez-Alvarado
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Colleen Miles
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. James W. Michelsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Heather A. Louis
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Dennis R. Winge
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Mary C. Beckerle
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Michael F. Summers
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Pérez-Alvarado, G., Miles, C., Michelsen, J. et al. Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP. Nat Struct Mol Biol 1, 388–398 (1994). https://doi.org/10.1038/nsb0694-388

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb0694-388

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