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
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).
Schatz, D.G., Oettinger, M.A. & Baltimore, D. The V(D)J recombination activating gene RAG1. Cell 59, 1035–1048 (1989).
Lewis, S.M. The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Advan. Immunol. 56, 27–150 (1994).
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).
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).
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).
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).
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).
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).
Rodgers, K.K. et al. A zinc-binding domain involved in the dimerization of RAG1. J. Mol. Biol. 260, 70–84 (1996).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Marmorstein, R., Carey, M., Ptashne, M. & Harrison, S.C. DNA recognition by GAL4: structure of a protein-DNA complex. Nature 356, 408–414 (1992).
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).
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).
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).
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).
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).
Coleman, J.E. Zinc proteins: enzymes, storage proteins, transcription factors, and replication proteins. Annu. Rev. Biochem. 61, 897–946 (1992).
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).
LOOK. Molecular Applications Group, Palo Alto, CA 94303.
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).
Berg, J.M. Zinc fingers and other metal-binding domains. J. Biol. Chem. 265, 6513–6516 (1990).
Pavelotich, N., Pabo, C. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science 252, 809–817 (1991)
Schwabe, J.W.R. & Klug, A. Zinc mining for protein domains. Nature Struct. Biol. 1, 345–349 (1994).
Connolly, M.L. Solvent-Accessible Surfaces of Proteins and Nucleic Acids. Science 221, 709–713 (1983).
Connolly, M.L. Computation of Molecular Volume. J. Am. Chem. Soc. 107, 1118–1124 (1985).
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).
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).
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).
Otwinowski, Z. in CCP4 Study Weekend (eds. Sawyer, L, Isaacs, N. & Bailey, S.) 56–62 (SERC Daresbury laboratory, England; 1993).
Minor, W. XDISPLAYF program.(Purdue University; 1993).
Sheldrick, G.M. Phase annealing in SHELX-90: Direct methods for larger structures. Acta Crystallogr. A46, 467–473 (1990).
Friedman, A.M., Fischmann, T.O., Shamoo, Y. & Ealick, S. in American Crystallographic Association Annual Meeting (Atlanta, Georgia; 1994).
Collaborative Computational Project, N. The CCP4 Suite: Programs for protein crystallography. Acta Crystallogr. D50, 760–763 (1994).
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).
Brunger, A.T. X-PLOR Version 3.843. (Yale Univ. Press, New Haven, CT, 1992).
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).
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).
Rould, M.A. Screening for Heavy-Atom Derivatives and Obtaining Accurate Isomorphous Differences. Meth. Enz. 276, 461–472.
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).
Carson, M. & Bugg, C.E. Algorythm for Ribbon Models of Proteins. J. Mol. Graphics 4, 121–122 (1986).
Ball, L.J. et al. Zinc coordination in the DNA-binding domain of the yeast transcriptional activator PPR1. FEBS Lett. 358, 278–282 (1995).
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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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DOI: https://doi.org/10.1038/nsb0797-586
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