Self-association and conformational properties of RAG1: Implications for formation of the V(D)J recombinase

Nucleic Acids Research

Volumn 31, Issue 7, 2003, Pages 2014-2023

  Godderz, LeAnn J ^a   Rahman, Negar S ^a   Risinger, George M ^a   Arbuckle, Janeen L ^a   Rodgers, Karla K ^a  

^a UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; DNA; RAG1 PROTEIN; RAG2 PROTEIN; RECOMBINASE; SODIUM CHLORIDE; TETRAMER;

ALPHA HELIX; CIRCULAR DICHROISM; CONTROLLED STUDY; DNA CLEAVAGE; ELECTRICITY; GEL MOBILITY SHIFT ASSAY; GENETIC RECOMBINATION; IONIC STRENGTH; LIGHT SCATTERING; MOLECULAR WEIGHT; NONHUMAN; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN DNA BINDING; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; REVIEW; STRUCTURE ACTIVITY RELATION;

ANIMALS; CELL LINE; CIRCULAR DICHROISM; DIMERIZATION; DNA NUCLEOTIDYLTRANSFERASES; DNA-BINDING PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENE REARRANGEMENT; HOMEODOMAIN PROTEINS; HUMANS; MICE; NUCLEAR PROTEINS; OLIGONUCLEOTIDES; OSMOLAR CONCENTRATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; VDJ RECOMBINASES;

MURINAE;

EID: 0037388110     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg281     Document Type: Review

References (41)

1. Lewis,S.M. (1994) The mechanism of V(D)J joining: lessons from molecular, immunological and comparative analyses. Adv. Immunol., 56, 27-150.
2. Fugmann,S.D., Lee,A.I., Shockett,P.E., Villey,I.J. and Schatz,D.G. (2000) The RAG proteins and V(D)J recombination: complexes, ends and transposition. Annu. Rev. Immunol., 18, 495-527.
3. Gellert,M. (2002) V(D)J recombination: RAG proteins, repair factors and regulation. Annu. Rev. Biochem., 71, 101-132.
4. Schatz,D.G., Oettinger,M.A. and Baltimore,D. (1989) The V(D)J recombination activating gene, RAG-1. Cell, 59, 1035-1048.
5. Oettinger,M.A., Schatz,D.G., Gorka,C. and Baltimore,D. (1990) RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science, 248, 1517-1523.
6. McBlane,J.F., van Gent,D.C., Ramsden,D.A., Romeo,C., Cuomo,C.A., Gellert,M. and 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.
7. Ma,Y., Pannicke,U., Schwarz,K. and Lieber,M.R. (2002) Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell, 108, 781-794.
8. Agrawal,A. and Schatz,D.G. (1997) RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination. Cell, 89, 43-53.
9. Hiom,K. and Gellert,M. (1998) Assembly of a 12/23 paired signal complex: a critical control point in V(D)J recombination. Mol. Cell, 1, 1011-1019.
10. Silver,D.P., Spanopoulou,E., Mulligan,R.C. and 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.
11. Sadofsky,M.J., Hesse,J.E., McBlane,J.F. and Gellert,M. (1993) Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucleic Acids Res., 21, 5644-5650.
12. Sadofsky,M.J., Hesse,J.E. and Gellert,M. (1994) Definition of a core region of RAG-2 that is functional in V(D)J recombination. Nucleic Acids Res., 22, 1805-1809.
13. Cuomo,C.A. and Oettinger,M.A. (1994) Analysis of regions of RAG-2 important for V(D)J recombination. Nucleic Acids Res., 22, 1810-1814.
14. Kim,D.R., Dai,Y., Mundy,C.L., Yang,W. and Oettinger,M.A. (1999) Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev., 13, 3070-3080.
15. Landree,M.A., Wibbenmeyer,J.A. and Roth,D.B. (1999) Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination. Genes Dev., 13, 3059-3069.
16. Fugmann,S.D., Villey,I.J., Ptaszek,L.M. and Schatz,D.G. (2000) Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex. Mol. Cell, 5, 97-107.
17. Haren,L., Ton-Hoang,B. and Chandler,M. (1999) Integrating DNA: transposases and retroviral integrases. Annu. Rev. Microbiol., 53, 245-281.
18. Akamatsu,Y. and Oettinger,M.A. (1998) Distinct roles of RAG1 and RAG2 in binding the V(D)J recombination signal sequences. Mol. Cell. Biol., 18, 4670-4678.
19. Rodgers,K.K., Villey,I.J., Ptaszek,L., Corbett,E., Schatz,D.G. and Coleman,J.E. (1999) A dimer of the lymphoid protein RAG1 recognizes the recombination signal sequence and the complex stably incorporates the high mobility group protein HMG2. Nucleic Acids Res., 27, 2938-2946.
20. Spanopoulou,E., Zaitseva,F., Wang,F.-H., Santagata,S., Baltimore,D. and Panayotou,G. (1996) The homeodomain region of Rag-1 reveals the parallel mechanisms of bacterial and V(D)J recombination. Cell, 87, 263-276.
21. Difilippantonio,M.J., McMahan,C.J., Eastman,Q.M., Spanopoulou,E. and Schatz,D.G. (1996) RAG1 mediates signal sequence recognition and recruitment of RAG2 in V(D)J recombination. Cell, 87, 253-262.
22. Arbuckle,J.L., Fauss,L.J., Simpson,R., Ptaszek,L.M. and Rodgers,K.K. (2001) Identification of two topologically independent domains in RAG1 and their role in macromolecular interactions relevant to V(D)J recombination. J. Biol. Chem., 276, 37093-37101.
23. Swanson,P.C. and Desiderio,S. (1999) RAG-2 promotes heptamer occupancy by RAG-1 in the assembly of a V(D)J initiation complex. Mol. Cell. Biol., 19, 3674-3683.
24. Eastman,Q.M., Villey,I.J. and Schatz,D.G. (1999) Detection of RAG protein-V(D)J recombination signal interactions near the site of DNA cleavage by UV cross-linking. Mol. Cell. Biol., 19, 3788-3797.
25. Yu,K. and Lieber,M.R. (2000) The nicking step in V(D)J recombination is independent of synapsis: implications for the immune repertoire. Mol. Cell. Biol., 20, 7914-7921.
26. Bailin,T., Mo,X. and Sadofsky,M.J. (1999) A RAG1 and RAG2 tetramer complex is active in cleavage in V(D)J recombination. Mol. Cell. Biol., 19, 4664-4671.
27. Mundy,C.L., Patenge,N., Matthews,A.G.W. and Oettinger,M.A. (2002) Assembly of the RAG1/RAG2 synaptic complex. Mol. Cell. Biol., 22, 69-77.
28. Swanson,P.C. (2002) A RAG-1/RAG-2 tetramer supports 12/23-regulated synapsis, cleavage and transposition of V(D)J recombination signals. Mol. Cell. Biol., 22, 7790-7801.
29. Wen,J., Arakawa,T. and Philo,J.S. (1996) Size-exclusion chromatography with on-line light-scattering, absorbance and refractive index detectors for studying proteins and their interactions. Anal. Biochem., 240, 155-166.
30. Rodgers,K.K., Bu,Z., Fleming,K.G., Schatz,D.G., Engelman,D.M. and Coleman,J.E. (1996) A zinc-binding domain involved in the dimerization of RAG1. J. Mol. Biol., 260, 70-84.
31. Sreerama,N. and Woody,R.W. (2000) Estimation of protein secondary structure from CD spectra: Comparison of CONTIN, SELCON and CDSSTR methods with an expanded reference set. Anal. Biochem., 287, 252-260.
32. Coleman,J., Eaton,S., Merkel,G., Skalka,A.M. and Laue,T. (1999) Characterization of the self association of avian sarcoma virus integrase by analytical ultracentrifugation. J. Biol. Chem., 274, 32842-32846.
33. Deprez,E., Tauc,P., Leh,H., Mouscadet,J.F., Auclair,C. and Brochon,J.C. (2000) Oligomeric states of the HIV-1 integrase as measured by time-resolved fluorescence anisotropy. Biochemistry, 39, 9275-9284.
34. Bellon,S.F., Rodgers,K.K., Schatz,D.G., Coleman,J.E. and Steitz,T.A. (1997) Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nature Struct. Biol., 4, 586-591.
35. Junker,M., Rodgers,K.K. and Coleman,J.E. (1998) Zinc as a structural and folding element of proteins which interact with DNA. Inorg. Chim. Acta, 275-276, 481-492.
36. Pelton,J.T. and McLean,L.R. (2000) Spectroscopic methods for analysis of protein secondary structure. Anal. Biochem., 277, 167-176.
37. Ciubotaru,M., Ptaszek,L.M., Baker,G.A., Baker,S.N., Bright,F.V. and Schatz,D.G. (2003) RAG1-DNA binding in V(D)J recombination: Specificity and DNA-induced conformational changes revealed by fluorescence and CD spectroscopy. J. Biol. Chem., 278, 5584-5596.
38. Swanson,P.C. and Desiderio,S. (1998) V(D)J recombination signal recognition: Distinct, overlapping DNA-protein contacts in complexes containing RAG1 with and without RAG2. Immunity, 9, 115-125.
39. Landree,M.A., Kale,S.B. and Roth,D.B. (2001) Functional organization of single and paired V(D)J cleavage complexes. Mol. Cell. Biol., 21, 4256-4264.
40. Lin,W.-C. and Desiderio,S. (1994) Cell cycle regulation of V(D)J recombination-activating protein RAG-2. Proc. Natl Acad. Sci. USA, 91, 2733-2737.
41. Spanopoulou,E., Cortes,P., Shih,C., Huang,C.M., Silver,D.P., Svec,P. and Baltimore,D. (1995) Localization, interaction and RNA binding properties of the V(D)J recombination-activating proteins RAG1 and RAG2. Immunity, 3, 715-726.