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

Abstract

The crystal structure of the dimerization domain of the V(D)J recombination-activating protein, RAG1, was solved using zinc anomalous scattering. The structure reveals an unusual combination of multi-class zinc-binding motifs, including a zinc RING finger and a C2H2 zinc finger, that together form a single structural domain. The domain also contains a unique zinc binuclear cluster in place of a normally mononuclear zinc site in the RING finger. Together, four zinc ions help organize the entire domain, including the two helices that form the dimer interface.

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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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Bellon, S., Rodgers, K., Schatz, D. et al. Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nat Struct Mol Biol 4, 586–591 (1997). https://doi.org/10.1038/nsb0797-586

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