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Originally published In Press as doi:10.1074/jbc.M105988200 on July 30, 2001

J. Biol. Chem., Vol. 276, Issue 40, 37093-37101, October 5, 2001
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Identification of Two Topologically Independent Domains in RAG1 and Their Role in Macromolecular Interactions Relevant to V(D)J Recombination*

Janeen L. ArbuckleDagger , LeAnn J. FaussDagger , Rosemarie SimpsonDagger §, Leon M. Ptaszek||, and Karla K. RodgersDagger **

From the Dagger  Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73190 and the  Ruttenberg Cancer Center, Mount Sinai School of Medicine of New York University, New York, New York 10029

V(D)J recombination is instigated by the recombination-activating proteins RAG1 and RAG2, which catalyze site-specific DNA cleavage at the border of the recombination signal sequence (RSS). Although both proteins are required for activity, core RAG1 (the catalytically active region containing residues 384-1008 of 1040) alone displays binding specificity for the conserved heptamer and nonamer sequences of the RSS. The nonamer-binding region lies near the N terminus of core RAG1, whereas the heptamer-binding region has not been identified. Here, potential domains within core RAG1 were identified using limited proteolysis studies. An iterative procedure of DNA cloning, protein expression, and characterization revealed the presence of two topologically independent domains within core RAG1, referred to as the central domain (residues 528-760) and the C-terminal domain (residues 761-980). The domains do not include the nonamer-binding region but rather largely span the remaining relatively uncharacterized region of core RAG1. Characterization of macromolecular interactions revealed that the central domain bound to the RSS with specificity for the heptamer and contained the predominant binding site for RAG2. The C-terminal domain bound DNA cooperatively but did not show specificity for either conserved RSS element. This domain was also found to self-associate, implicating it as a dimerization domain within RAG1.

* This work was supported by Research Project Grant RPG-00-032-01-CIM from the American Cancer Society, an Oklahoma Center for Advancement in Science and Technology award for project number HR99-040 and funds from the Presbyterian Health Foundation.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

§ Present address: Sangamo Biosciences, Inc., Richmond, CA 94804.

|| Present address: Section of Immunobiology, Yale University School of Medicine, New Haven, CT 06520.

** To whom correspondence should be addressed. Tel.: 405-271-2227, Ext. 1248; Fax: 405-271-3139; E-mail: Karla-Rodgers@ouhsc.edu.

Copyright © 2001 by The American Society for Biochemistry and Molecular Biology, Inc.
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