Structural studies of sequential DNA cleavage by RAG1/RAG2 proteins in V(D)J recombination

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Advances in our research program on the structural analysis of the RAG1-RAG2 protein have provided a fuller understanding of its functions in the past year. We now have obtained detailed structures representing all stages of the RAG1/2 cleavage of DNA, and find some unexpected features. The previously reported unwinding of several base pairs of DNA adjacent to the recombination signal sequence, found to be necessary to activate the DNA for cleavage, is accompanied by the unwound strands meshing together in a DNA zipper with alternating bases from opposite strand interleaved and stabilized by stacking forces. This novel structure is clearly more stable in the non-aqueous protein interior than a strand-separated one. As RAG1/2 has a secondary transposase activity, we have also determined the structure of its strand-transfer intermediate in which it has captured a target DNA but not yet released the product. With RAG, this intermediate requires much more distortion of target DNA than in related transposases, probably explaining why RAG is an inefficient transposase, as is compatible with its primary activity as a DNA-cutting enzyme. Transposition in the context of immune system cells would most likely be harmful. Two papers describing these results have been submitted for publication. As these results were obtained with truncated but active forms of the RAG proteins, we are now pursuing structures of longer forms, which contain regulatory elements of the RAG1 N-terminus and the RAG2 C-terminus that control RAG activity.