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V(D)J recombination signal recognition: distinct, overlapping DNA-protein contacts in complexes containing RAG1 with
1Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
Abstract:
Protein interactions with V(D)J recombination signal sequences (RSSs) were mapped in complexes containing RAG1 with (M1/2) or without (M1) RAG2. In both complexes, RAG interactions with the DNA backbone are biased toward one side of the helix; nonamer contacts resemble those of Hin with hixL. In the M1 complex, DNA contacts are centered on the nonamer. In the M1/2 complex, protein-RSS interactions extend through the spacer and into the nonamer-proximal portion of the heptamer. Chemical modifications near the heptamer-coding junction are overrepresented in the M1/2 complex, providing evidence for perturbation of DNA structure in this region. Thus, while RAG1 alone can bind the nonamer, RAG2 is required for heptamer occupancy.