Cracking the DNA Code for V(D)J Recombination

• Published in: Molecular cell Vol. 70; no. 2; pp. 358 - 370.e4
• Main Authors: Kim, Min-Sung, Chuenchor, Watchalee, Chen, Xuemin, Cui, Yanxiang, Zhang, Xing, Zhou, Z. Hong, Gellert, Martin, Yang, Wei
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19.04.2018
• Subjects: Binding Sites; CA/TG dinucleotides; Catalysis; Cryoelectron Microscopy; Crystallography, X-Ray; DNA - genetics; DNA - metabolism; DNA - ultrastructure; DNA bending; DNA Breaks, Double-Stranded; DNA hairpin; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; DNA-Binding Proteins - ultrastructure; HEK293 Cells; HMGB1 Protein - genetics; HMGB1 Protein - metabolism; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; Homeodomain Proteins - ultrastructure; Humans; Models, Molecular; NBD; Nucleic Acid Conformation; polypurine tract; Protein Binding; Protein Conformation; SCID; Structure-Activity Relationship; V(D)J Recombination; NBD; polypurine tract; DNA hairpin; SCID; CA/TG dinucleotides; DNA bending
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2018.03.008

To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the “beyond 12/23” restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking. [Display omitted] •Structures of RAG1/2-DNA complexes are solved at 2.75 Å by X-ray and 3.17 Å by cryo-EM•RAG1/2 opens and closes like a nutcracker when binding and cleaving DNA•Location-sensitive bending of 60° and 150° in two RSS spacers is needed for cleavage•Hairpin structures and the catalytic process of DNA hairpin formation are revealed V(D)J recombination is an essential step in generating large numbers of different antibodies and T cell receptors for many vertebrates. Here, we show how the RAG1/2 protein recognizes and pairs two different DNA signals attached to the recombining gene fragments to initiate the necessary DNA double-strand breaks.