A zinc-binding domain involved in the dimerization of RAG1

Journal of Molecular Biology

Volumn 260, Issue 1, 1996, Pages 70-84

  Rodgers, Karla K ^a   Bu, Zimei ^a   Fleming, Karen G ^a   Schatz, David G ^b   Engelman, Donald M ^a   Coleman, Joseph E ^a  

^a YALE UNIVERSITY   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Analytical ultracentrifugation; C3HC4 zinc domains; RAG1; Small angle X ray scattering; V(D)J recombination

Indexed keywords

ARTICLE; GENE ACTIVATION; GENE SEQUENCE; GENETIC RECOMBINATION; IMMUNOGLOBULIN GENE; IMMUNOGLOBULIN VARIABLE REGION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION;

EID: 0030570467     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0382     Document Type: Article

References (51)

1. Bach, I., Rhodes, S. J., Pearse, R. V., Heinzel, T., Gloss, B., Scully, K. M., Sawchenko, P. E. & Rosenfeld, M. G. (1995). P-Lim, a LIM homeodomain F factor, is expressed during pituitary organ and cell commitment and synergizes with Pit-1. Proc. Natl Acad. Sci. USA, 92, 2720-2724.
2. 1H-nuclear magnetic resonance spectroscopy. J. Mol. Biol. 237, 201-211.
3. Berg, J. M. (1990). Zinc fingers and other metal-binding domains. J. Biol. Chem. 265, 6513-6516.
4. Borden, K. L. B., Boddy, M. N., Lally, J., O'Reilly, N. J., Martin, S., Howe, K., Solomon, E. & Freemont, P. S. (1995). The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto-oncoprotein PML. EMBO J. 14, 1532-1541.
5. Cheng, G., Cleary, A. M., Ye, Z.-s., Hong, D. I., Lederman, S. & Baltimore, D. (1995). Involvement of CRAF1, a relative of TRAF, in CD40 signaling. Science, 267, 1494-1498.
6. Cohn, E. J. & Edsall, J. T. (1943). Density and apparent specific volume of proteins. In Proteins, Amino Acids and Peptides as Ions and Dipolar Ions (Cohn, E. J. & Edsall, J. T., eds), pp. 370-381, Reinhold Publishing Corporation, New York.
7. Coleman, J. E. (1992). Zinc proteins: enzymes, storage proteins, transcription factors, and replication proteins. Annu. Rev. Biochem. 61, 897-946.
8. Cortes, P., Ye, Z. S. & Baltimore, D. (1994). RAG-1 interacts with the repeated amino acid motif of the human homologue of the yeast protein SRP1. Proc. Natl Acad. Sci. USA, 91, 7633-7637.
9. Cuomo, C. A. & Oettinger, M. A. (1994). Analysis of regions of RAG-2 important for V(D)J recombination. Nucl. Acids Res. 22, 1810-1814.
10. Engelman, D. M. & Moore, P. B. (1975). Determination of quaternary structure by small angle neutron scattering. Annu. Rev. Biophys. Bioeng. 4, 219-241.
11. Feuerstein, R., Wang, X., Song, D., Cooke, N. E. & Liebhaber, S. A. (1994). The LIM/double zinc-finger motif functions as a protein dimerization domain. Proc. Natl Acad. Sci. USA, 91, 10655-10659.
12. Frankel, A. D., Berg, J. M. & Pabo, C. O. (1987). Metal-dependent folding of a single zinc finger from transcription factor IIIA. Proc. Natl Acad. Sci. USA, 84, 4841-4845.
13. Freemont, P. S. (1993). The RING finger: a novel protein sequence motif related to the zinc finger. Ann. N.Y. Acad. Sci. 684, 174-192.
14. Freemont, P. S., Hanson, I. M. & Trowsdale, J. (1991). A novel cysteine-rich sequence motif. Cell, 64, 483-484.
15. Futreal, P. A., Liu, Q., Shattuck-Eidens, D., Cochran, C., Harshman, K., Tavtigian, S. et al. (1994). BRCA1 mutations in primary breast and ovarian carcinomas. Science, 266, 120-122.
16. 6 DNA-binding domain. Nature Struct. Biol. 2, 898-905.
17. Glatter, O. (1982). In Small Angle X-ray Scattering (Glatter, O. & Kratky, O., eds), pp. 119-165, Academic Press, London.
18. Gorlich, D., Prehn, S., Laskey, R. A. & Hartmann, E. (1994). Isolation of a protein that is essential for the first step of nuclear protein import. Cell, 79, 767-778.
19. Hsieh, C. & Lieber, M. R. (1992). CpG methylated minichromosomes become inaccessible for V(D)J recombination after undergoing replication. EMBO J. 11, 315-325.
20. Jasanoff, A., Kochoyan, M., Fraenkel, E., Lee, J. P. & Weiss, M. A. (1992). Aromatic-aromatic interactions in the zinc finger motif. Analysis of the two-dimensional nuclear magnetic resonance structure of a mutant domain. J. Mol. Biol. 225, 1035-1047.
21. Johnson, M. L., Correia, J. J., Yphantis, D. A. & Halvorson, H. R. (1981). Analysis of data from the analytical ultracentrifuge by nonlinear least-squares techniques. Biophys. J. 36, 575-588.
22. Kuntz, I. D. (1971). Hydration of macromolecules III. Hydration of polypeptides. J. Am. Chem. Soc. 93, 514-516.
23. Laue, T. M., Shah, B., Ridgeway, T. M. & Pelletier, S. L. (1992). Computer-aided interpretation of analytical sedimentation data for proteins. In Analytical Ultracentrifugation in Biochemistry and Polymer Science (Harding, S. E., Rowe, A. J. & Horton, J. C., eds), pp. 90-125, Royal Society of Chemistry, Cambridge, UK.
24. Leu, T. M. J. & Schatz, D. G. (1995). Rag-1 and Rag-2 are components of a high molecular weight complex and association of Rag-2 with this complex is Rag-1 dependent. Mol. Cell. Biol. 15, 5657-5670.
25. Lewis, S. M. (1994). The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Advan. Immunol. 56, 27-150.
26. Luisi, B. F., Xu, W. X., Otwinowski, Z., Freedman, L. P., Yamamoto, K. R. & Sigler, P. B. (1991). Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature, 352, 497-505.
27. Maina, C. V., Riggs, P. D., Grandea, A. G., Slatko, B. E., Moran, L. S., Tagliamonte, J. A., Reynolds, L. A. & Guan, C. D. (1988). An Escherichia coli vector to express and purify foreign proteins by fusion to and separation from maltose-binding protein. Gene, 74, 365-373.
28. McBlane, J. F., van Gent, D. C., Ramsden, D. A., Romeo, C., Cuomo, C. A., Geliert, M. & Oettinger, M. A. (1995). Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell, 83, 387-395.
29. McRorie, D. K. & Voelker, P. J. (1993). Self-associating Systems in the Analytical Ultracentrifuge. Beckman Instruments, Inc., Fullerton, CA.
30. Oettinger, M. A., Schatz, D. G., Gorka, C. & Baltimore, D. (1990). RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science, 248, 1517-1523.
31. 2 zinc finger from the human enhancer binding protein MBP-1. Biochemistry, 31, 3907-3917.
32. Pan, T. & Coleman, J. E. (1990). The DNA binding domain of GAL4 forms a binuclear metal ion complex. Biochemistry, 29, 3023-3029.
33. Parraga, G., Horvath, S. J., Eisen, A., Taylor, W. E., Hood, L., Young, E. T. & Klevit, R. E. (1988). Zinc-dependent structure of a single-finger domain of yeast ADRl. Science, 241, 1489-1492.
34. Pavletich, N. P. & Pabo, C. O. (1993). Crystal structure of a five-finger GLI-DNA domplex: new perspectives on zinc fingers. Science, 261, 1701-1707.
35. Perez-Alvarado, G. C., Miles, C., Michelson, J. W., Louis, H. A., Winge, D. R., Beckerle, M. C. & Summers, M. F. (1994). Structure of the C-terminal LIM domain from the cysteine rich protein CRP. Nature Struct. Biol. 1, 388-398.
36. Qian, X. & Weiss, M. A. (1992). Two-dimensional NMR studies of the zinc finger motif: solution structures and dynamics of mutant ZFY domains containing aromatic substitutions in the hydrophobic core. Biochemistry, 31, 7463-7476.
37. Rodgers, K. K. & Coleman, J. E. (1994). DNA binding and bending by the transcription factors GAL4(62*) and GAL4(149*). Protein Sci. 3, 608-619.
38. Rothe, M., Sarma, V., Dixit, V. M. & Goeddel, D. V. (1995). TRAF2-mediated activation of NF-KB by TNF receptor 2 and CD40. Science, 269, 1424-1427.
39. Sadofsky, M. J., Hesse, J. E., McBlane, J. F. & Geliert, M. (1993). Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucl. Acids Res. 21, 5644-5650.
40. Sadofsky, M. J., Hesse, J. E. & Gellert, M. (1994). Definition of a core region of RAG-2 that is functional in V(D)J recombination. Nucl. Acids Res. 22, 1805-1809.
41. Schatz, D. G. & Leu, T. M. J. (1996). Rag-1 and rag-2: biochemistry and protein interactions. In Molecular Analysis of DNA Rearrangements in the Immune System (Jessberger, R. & Lieber, M. R., eds), Springer-Verlag, Heidelberg. In the press.
42. Schatz, D. G., Oettinger, M. A. & Baltimore, D. (1989). The V(D)J recombination activating gene, RAG-1. Cell, 59, 1035-1048.
43. Schmeichel, K. L. & Beckerle, M. C. (1994). The LIM domain is a modular protein-binding interface. Cell, 79, 211-219.
44. Schwabe, J. W. R. & Klug, A. (1994). Zinc mining for protein domains. Nature Struct. Biol. 1, 345-349.
45. Silver, D. P., Spanopoulou, E., Mulligan, R. C. & Baltimore, D. (1993). 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.
46. Semenyuk, A. V. & Svergun, D. I. (1991). GNOM-a program package from small-angle scattering data processing. J. Appl. Crystallog. 24, 537-540.
47. Spanopoulou, E., Cortes, P., Shih, C., Huang, E., Silver, D. P., Svec, P. & Baltimore, D. (1995). Localization, interaction and RNA binding properties of the V(D)J recombination-activating proteins Rag-1 and Rag-2. Immunity, 3, 715-726.
48. Spurlino, J. C., Lu, G.-Y. & Quiocho, F. A. (1991). The 2.3-Å resolution structure of the maltose-or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. J. Biol. Chem. 266, 5202-5219.
49. Sreerama, N. & Woody, R. W. (1993). A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal. Biochem. 209, 32-44.
50. Stafford, W. (1992). Boundary analysis in sedimentation transport experiments: a procedure for obtaining sedimentation coefficient distributions using the time derivative of the concentration profile. Anal. Biochem. 203, 295-391.
51. van Gent, D. C., McBlane, J. F., Ramsden, D. A., Sadofsky, M. J., Hesse, J. E. & Geliert, M. (1995). Initiation of V(D)J recombination in a cell-free system. Cell, 81, 925-934.