Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster (original) (raw)

References

  1. Oettinger, M.A., Schatz, D.G., Gorka, C. & Baltimore, D. RAG1 and RAG2, Adjacent genes that synergistically activate V(D)J recombination. Science 248, 1517–1523 (1990).
    CAS PubMed Google Scholar
  2. Schatz, D.G., Oettinger, M.A. & Baltimore, D. The V(D)J recombination activating gene RAG1. Cell 59, 1035–1048 (1989).
    CAS PubMed Google Scholar
  3. Lewis, S.M. The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Advan. Immunol. 56, 27–150 (1994).
    CAS Google Scholar
  4. Eastman, Q.M., Leu, T.M. & Schatz, D.G. Initiation of V(D)J recombination in vitro obeying the 12/23 rule. Nature 380, 85–88 (1996).
    CAS PubMed Google Scholar
  5. vanGent, D.C., Ramsden, D.A. & Gellert, M. The RAG1 and RAG2 proteins establish the 12/23 rule in V(D)J recombination. Cell 85, 107–113 (1996).
    CAS Google Scholar
  6. Sadofsky, M.J., Hesse, J.E., McBlane, J.F. & Gellert, M. Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucleic Acids Res. 21, 5644–5650 (1993).
    CAS PubMed PubMed Central Google Scholar
  7. Sadofsky, M.J., Hesse, J.E. & Gellert, M. Definition of a core region of RAG-2 that is functional in V(D)J recombination. Nucleic Acids Res. 22, 1805–1809 (1994).
    CAS PubMed PubMed Central Google Scholar
  8. Cuomo, C.A. & Oettinger, M.A. Analysis of regions of RAG-2 important for V(D)J recombination. Nucleic Acids Res. 22, 1810–1814 (1994).
    CAS PubMed PubMed Central Google Scholar
  9. Silver, D.P., Spanopoulou, E., Mulligan, R.C. & Baltimore, D. Dispensable sequence motifs in the RAG-1 and RAG-2 genes for plasmid V(D)J recombination. Proc. Natl. Acad. Sci. USA 90, 6100–6104 (1993).
    CAS PubMed Google Scholar
  10. Rodgers, K.K. et al. A zinc-binding domain involved in the dimerization of RAG1. J. Mol. Biol. 260, 70–84 (1996).
    CAS PubMed Google Scholar
  11. Rodgers, K.K. & Fleming, K.G. Metal-dependent structure and self association of the RAG1 zinc-binding domain. In Techniques in Protein Chemistry VIII (ed. Marshak, D.R.) in the press (Academic Press, Orlando, Florida, 1997).
    Google Scholar
  12. Schatz, D.G. & Leu, T.M.J. Rag-1 and rag-2: biochemistry and protein interactions, in Molecular Analysis of DNA Rearrangements in the Immune System (eds. Jessberger, R. & Lieber, M.R.) 11–29 (Springer-Verlag, Heidelberg, 1996).
    Google Scholar
  13. Spanopoulou, E. et al. The homeodomain region of Rag-1 reveals the parallel mechanisms of bacterial and V(D)J recombination. Cell 87, 263–276 (1996).
    CAS PubMed Google Scholar
  14. Difilippantonio, M.J., McMahan, C.J., Eastman, Q.M., Spanopoulou, E. & Schatz, D.G. RAG1 mediates signal sequence recognition and recruitment of RAG2 in V(D)J recombination. Cell 87, 253–262 (1996).
    CAS PubMed Google Scholar
  15. Saurin, A.J., Borden, K.L.B., Boddy, M.N. & Freemont, P.S. Does this have a familiar RING? Trends Biochem. Sci. 21, 208–214 (1996).
    CAS PubMed Google Scholar
  16. Barlow, P.N., Luisi, B., Milner, A., Elliot, M. & Everett, R. Structure of the C3HC4 domain by 1H-Nuclear Magnetic Resonance spectroscopy. J. Mol. Biol. 237, 201–211 (1994).
    CAS PubMed Google Scholar
  17. Borden, K.L.B. et al. The solution structure of the RING finger domain from the Acute Promyelocytic Leukaemia proto-oncoprotein PML. EMBO J. 14, 1532–1541 (1995).
    CAS PubMed PubMed Central Google Scholar
  18. Messerle, B.A., Schaffer, A., Vasak, M., Kagi, J.H. & Wuthrich, K. Three-dimensional structure of human [113Cd7]metallothionein-2 in solution determined by nuclear magnetic resonance spectroscopy. J. Mol. Biol. 214, 765–779 (1990).
    CAS PubMed Google Scholar
  19. Gardner, K.H., Anderson, S.F. & Coleman, J.E. Solution structure of the Kluyveromyces lactis LAC9 Cd2Cys6 DNA-binding domain. Nature Struct. Biol. 2, 898–905 (1995).
    CAS PubMed Google Scholar
  20. Marmorstein, R., Carey, M., Ptashne, M. & Harrison, S.C. DNA recognition by GAL4: structure of a protein-DNA complex. Nature 356, 408–414 (1992).
    CAS PubMed Google Scholar
  21. Marmorstein, R. & Harrison, S.C. Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster. Genes Dev. 8, 2504–2512 (1994).
    CAS PubMed Google Scholar
  22. 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).
    Google Scholar
  23. 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).
    CAS PubMed Google Scholar
  24. Shirakawa, M. et al. Assignment of 1H, 15N, 13C resonances, identification of elements of secondary structure and determination of the global fold of the DNA-binding domain of GAL4. Biochemistry 32, 2144–2153 (1993).
    CAS PubMed Google Scholar
  25. Timmerman, J.E. et al. 1H, 15N resonance assignments and three-dimensional structure of CYP1 (HAP1) DNA-binding domain. J. Mol. Biol. 259, 792–804 (1996).
    CAS PubMed Google Scholar
  26. Coleman, J.E. Zinc proteins: enzymes, storage proteins, transcription factors, and replication proteins. Annu. Rev. Biochem. 61, 897–946 (1992).
    CAS PubMed Google Scholar
  27. Bernstein, R.M., Schluter, S.F., Bernstein, H. & Marchalonis, J.J. Primordial emergence of the recombination activating gene 1 (RAG1): Sequence of the complete shark gene indicates homology to microbial integrases. Proc. Natl. Acad. Sci. USA 93, 9454–9459 (1996).
    CAS PubMed Google Scholar
  28. LOOK. Molecular Applications Group, Palo Alto, CA 94303.
  29. Flores, T.P., Orengo, C.A., Moss, D.S. & Thornton, J.M. Comparison of conformational characteristics in structurally similar protein pairs. Protein Science 2, 1811–1826 (1993).
    CAS PubMed PubMed Central Google Scholar
  30. Berg, J.M. Zinc fingers and other metal-binding domains. J. Biol. Chem. 265, 6513–6516 (1990).
    CAS PubMed Google Scholar
  31. Pavelotich, N., Pabo, C. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science 252, 809–817 (1991)
    Google Scholar
  32. Schwabe, J.W.R. & Klug, A. Zinc mining for protein domains. Nature Struct. Biol. 1, 345–349 (1994).
    CAS PubMed Google Scholar
  33. Connolly, M.L. Solvent-Accessible Surfaces of Proteins and Nucleic Acids. Science 221, 709–713 (1983).
    CAS Google Scholar
  34. Connolly, M.L. Computation of Molecular Volume. J. Am. Chem. Soc. 107, 1118–1124 (1985).
    CAS Google Scholar
  35. Spanopoulou, E. et al. Localization, interaction, and RNA binding properties of the V(D)J recombination-activating proteins RAG1 and RAG2. Immunity 3, 715–726 (1995).
    CAS PubMed Google Scholar
  36. Ramsden, D.A., McBlane, J.F., vanGent, D.C. & Gellert, M. Distinct DNA sequence and structure requirements for the two steps of V(D)J recombination signal cleavage. EMBO J. 15, 3197–3206 (1996).
    CAS PubMed PubMed Central Google Scholar
  37. Borden, K.L.B. & Freemont, P.S. The RING finger domain - a recent example of a sequence-structure family. Curr. Opin. Struct. Biol. 6, 395–401 (1996).
    CAS PubMed Google Scholar
  38. Otwinowski, Z. in CCP4 Study Weekend (eds. Sawyer, L, Isaacs, N. & Bailey, S.) 56–62 (SERC Daresbury laboratory, England; 1993).
    Google Scholar
  39. Minor, W. XDISPLAYF program.(Purdue University; 1993).
  40. Sheldrick, G.M. Phase annealing in SHELX-90: Direct methods for larger structures. Acta Crystallogr. A46, 467–473 (1990).
    CAS Google Scholar
  41. Friedman, A.M., Fischmann, T.O., Shamoo, Y. & Ealick, S. in American Crystallographic Association Annual Meeting (Atlanta, Georgia; 1994).
    Google Scholar
  42. Collaborative Computational Project, N. The CCP4 Suite: Programs for protein crystallography. Acta Crystallogr. D50, 760–763 (1994).
  43. Ramakrishnan, V., Finch, J.T., Graziano, V., Lee, P.L. & Sweet, R.M. Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature 362, 219 (1993).
    CAS PubMed Google Scholar
  44. Brunger, A.T. X-PLOR Version 3.843. (Yale Univ. Press, New Haven, CT, 1992).
  45. Burling, F.T., Weis, W.I., Flanerty, K.M. & Brunger, A.T. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science 271, 72–77 (1996).
    CAS PubMed Google Scholar
  46. Jones, T.A. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110 (1991).
    Google Scholar
  47. Rould, M.A. Screening for Heavy-Atom Derivatives and Obtaining Accurate Isomorphous Differences. Meth. Enz. 276, 461–472.
  48. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993).
    CAS Google Scholar
  49. Carson, M. & Bugg, C.E. Algorythm for Ribbon Models of Proteins. J. Mol. Graphics 4, 121–122 (1986).
    CAS Google Scholar
  50. Ball, L.J. et al. Zinc coordination in the DNA-binding domain of the yeast transcriptional activator PPR1. FEBS Lett. 358, 278–282 (1995).
    CAS PubMed Google Scholar

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