The products of recombination activating genes (RAG) 1 and 2 mediate the assembly of antigen receptor genes during lymphocyte development in a process known as V(D)J recombination. Lack of structural information for the RAG proteins has hindered mechanistic studies of this reaction. We report here the crystal structure of an essential DNA-binding domain of the RAG1 catalytic core bound to its nonamer DNA recognition motif. The RAG1 nonamer-binding domain (NBD) forms a tightly interwoven dimer that binds and synapses two nonamer elements, with each NBD making contact with both DNA molecules. Biochemical and biophysical experiments confirm that the two nonamers are in close proximity in the RAG1/2-DNA synaptic complex and demonstrate the functional importance of the protein-DNA contacts revealed in the structure. These findings reveal a previously unsuspected function for the NBD in DNA synapsis and have implications for the regulation of DNA binding and cleavage by RAG1/2.

During V(D)J recombination, recombination activating gene proteins RAG1 and RAG2 generate DNA double strand breaks within a paired complex (PC) containing two complementary recombination signal sequences (RSSs), the 12RSS and 23RSS, which differ in the length of the spacer separating heptamer and nonamer elements. Despite the central role of the PC in V(D)J recombination, little is understood about its structure. Here, we use fluorescence resonance energy transfer to investigate the architecture of the 23RSS in the PC. Energy transfer was detected in 23RSS substrates in which the donor and acceptor fluorophores flanked the entire RSS, and was optimal under conditions that yield a cleavage-competent PC. The data are most easily explained by a dramatic bend in the 23RSS that reduces the distance between these flanking regions from >160 Å in the linear substrate to <80 Å in the PC. Analysis of multiple fluorescent substrates together with molecular dynamics modeling yielded a model in which the 23RSS adopts a U shape in the PC, with the spacer located centrally within the bend. We propose that this large bend facilitates simultaneous recognition of the heptamer and nonamer, is critical for proper positioning of the active site and contributes to the 12/23 rule.

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The assembly of the gene segments coding for the variable portions of lymphocyte antigen receptors (immunoglobulins and T-cell receptors) occurs via a somatic recombination reaction known as V(D)J recombination. This process is mediated by two lymphoid cell-specific factors, RAG1 and RAG2 (recombination-activating gene products), that perform DNA cleavage at a pair of recombination signal sequences (RSSs) flanking the coding segments to be joined. RSSs consist of short palindromic heptamer and A/T-rich nonamer elements separated by a less well conserved spacer of 12 or 23 bp (12-RSS and 23-RSS). In vivo, recombination occurs most efficiently with a 12/23 RSS pair, a phenomenon referred to as the 12/23 rule.Under appropriate conditions in vitro, the RAG proteins together with high-mobility-group protein HMGB1 or HMGB2 perform coupled DNA cleavage of RSS substrates in accordance with the 12/23 rule (16). This process is thought to be initiated by the binding of the RAG recombinase to one RSS, followed by the capture of a second RSS, thus assembling the synaptic, or paired, complex (PC) (22, 28). HMGB1 and HMGB2 proteins play critical roles in vitro in facilitating the binding of the RAG proteins to the 23-RSS and the formation of the PC (15, 16), activities thought to rely on their ability to recognize bent or distorted DNA structures (3, 7). DNA cleavage takes place in two steps: a nick is first introduced between the heptamer and the coding DNA, and the 3Ј hydroxyl group thus liberated then attacks the other strand of the duplex to generate a covalently sealed hairpin coding end and a blunt signal end (16). Nicking can occur before or after synapsis, but hairpin formation occurs coordinately at the two RSSs within the PC (15). The PC is thus a critical intermediate in which the recombining partners are chosen and DNA double-strand breaks are made.Numerous studies have identified functionally important residues and domains within the catalytically essential, or core, region of RAG1 (10): an N-terminal nonamer binding domain that interacts with the RSS nonamer, a central domain that interacts with RAG2 and the heptamer and contains two of three acidic residues thought to contribute to the RAG active site, and a C-terminal domain with dimerization and nonspecific DNA binding activity and the third active-site residue. Less is known about the RAG2 core region.The structure of the PC is poorly understood. The PC is thought to contain two (37) or more than two (28) RAG1 monomers, two monomers of RAG2 (28,37), and an unknown number of HMGB1 or HMGB2 subunits. The nonamer binding and catalytic domains that interact with a particular RSS are contributed by different RAG1 monomers (36). This and the dependence of hairpin formation upon synapsis suggest careful coordination between the catalytic events at the two RSSs, a possibility supported by the finding that nicking at one RSS is required for hairpin formation at the partner RSS (41).Very little is known about the structure of the two DNA molecules in the PC. RAG1/2 an...

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The RAG1 and RAG2 proteins together constitute the nuclease that initiates the assembly of immunoglobulin and T cell receptor genes in a reaction known as V(D)J recombination. RAG1 plays a central role in recognition of the recombination signal sequence (RSS) by the RAG1/2 complex. To investigate the parameters governing the RAG1-RSS interaction, the murine core RAG1 protein (amino acids 377-1008) fused to a short Strep tag has been purified to homogeneity from bacteria. The Strep-RAG1 (StrRAG1) protein exists as a dimer at a wide range of protein concentrations (25-500 nM) in the absence of DNA and binds with reasonably high affinity and specificity (apparent K D ‫؍‬ 41 nM) to the RSS. Both electrophoretic mobility shift assays and polarization anisotropy experiments indicate that only a single StrRAG1-DNA species exists in solution. Anisotropy decay measured by frequency domain spectroscopy suggests that the complex contains a dimer of StrRAG1 bound to a single DNA molecule. Using measurements of protein intrinsic fluorescence and circular dichroism, we demonstrate that StrRAG1 undergoes a major conformational change upon binding the RSS. Steady-state fluorescence and acrylamide quenching studies reveal that this conformational change is associated with a repositioning of intrinsic protein fluorophores from a hydrophobic to a solvent-exposed environment. RSS-induced conformational changes of StrRAG1 may influence the interaction of RAG1 with RAG2 and synaptic complex formation.The genes encoding the variable domains of immunoglobulins or T cell receptors are generated during lymphocyte differentiation by a somatic recombination reaction known as V(D)J recombination (1). The reaction is initiated by DNA double strand breaks created at the junction between two coding segments (termed V, D, or J) and their flanking recombination signal sequences (RSSs). 1 Cleavage is followed by a complex repair process that results in imprecise joining of the two coding segments and typically precise joining of the two RSSs. The RSSs consist of two conserved sequence elements, the heptamer (consensus 5Ј-CACAGTG-3Ј) and the nonamer (consensus 5Ј-ACAAAAACC-3Ј), separated by a poorly conserved spacer sequence of either 12 or 23 base pairs. Efficient recombination occurs only between a 12-RSS and a 23-RSS, a phenomenon known as the 12/23 rule (for review, see Ref.2). Recognition of 12/23-RSSs and concerted cleavage at the RSScoding sequence border is performed by a complex of the RAG1 and RAG2 proteins (for reviews, see Ref. 3 and 4), the lymphoid-specific products of the recombination-activating genes RAG1 and RAG2 (5, 6). Binding and cleavage of DNA by the RAG1⅐RAG2 complex is facilitated by the ubiquitously expressed architectural DNA-binding proteins 8).Deletion mutagenesis has established the minimal "core" domains of murine RAG1 (residues 384 -1008 of the 1040 aa RAG1 protein; Fig. 1A) and RAG2 (residues 1-383 of the 527 aa RAG2 protein) required for recombination activity in transfected nonlymphoid cell lines (9 -12). Most bi...

V(D)J recombination requires binding and synapsis of a complementary (12/23) pair of recombination signal sequences (RSSs) by the RAG1 and RAG2 proteins, aided by a high-mobility group protein, HMG1 or HMG2. Double-strand DNA cleavage within this synaptic, or paired, complex is thought to involve DNA distortion or melting near the site of cleavage. Although V(D)J recombination normally occurs between RSSs located on the same DNA molecule (in cis), all previous studies that directly assessed RSS synapsis were performed with the two DNA substrates in trans. To overcome this limitation, we have developed a facilitated circularization assay using DNA substrates of reduced length to assess synapsis of RSSs in cis. We show that a 12/23 pair of RSSs is the preferred substrate for synapsis of cis RSSs and that the efficiency of pairing is dependent upon RAG1-RAG2 stoichiometry. Synapsis in cis occurs rapidly and is kinetically favored over synapsis of RSSs located in trans. This experimental system also allowed the generation of underwound DNA substrates containing pairs of RSSs in cis. Importantly, we found that the RAG proteins cleave such substrates substantially more efficiently than relaxed substrates and that underwinding may enhance RSS synapsis as well as RAG1/2-mediated catalysis. The energy stored in such underwound substrates may be used in the generation of DNA distortion and/or protein conformational changes needed for synapsis and cleavage. We propose that this unwinding is uniquely sensed during synapsis of an appropriate 12/23 pair of RSSs.The process of immunoglobulin and T-cell receptor gene rearrangement, known as V(D)J recombination, occurs during lymphocyte differentiation and plays a major role in diversifying these antigen receptors in jawed vertebrates (55). Two steps precede DNA double-strand cleavage by the RAG1/ RAG2 recombinase machinery. First, RAG1-RAG2 specifically bind to short DNA elements termed recombination signal sequences (RSSs) flanking the V, D, and J gene segments. RSSs are composed of two well-conserved sequences, a palindromic heptamer (consensus 5Ј-CACAGTG) and an A/T-rich nonamer (consensus 5Ј-ACAAAAACC) separated by a lesswell-conserved spacer region of 12 or 23 bp in length (41). The second step, the synapsis of a pair of RSSs, determines both the identity and the type of gene segments to be adjoined. It is within this paired complex that DNA double-strand breaks are introduced between the heptamer and flanking coding region (referred to as hairpin formation, because cleavage generates a covalently sealed hairpin structure at the end of each coding segment).In vivo, recombination occurs almost exclusively between gene segments flanked by a 12-and a 23-RSS (complementary RSSs) according to the 12/23 rule. The mechanisms enforcing this important restriction remain poorly understood at a molecular level. Biochemical experiments have revealed a more stringent adherence to the 12/23 rule in coupled cleavage assays (11,56,58) than in electrophoretic mobility shift assays that ass...

V(D)J recombination is initiated by RAG1 and RAG2, which together with HMGB1 bind to a recombination signal sequence (12RSS or 23RSS) to form the signal complex (SC) and then capture a complementary partner RSS, yielding the paired complex (PC). Little is known regarding the structural changes that accompany the SC to PC transition or the structural features that allow RAG to distinguish its two asymmetric substrates. To address these issues, we analyzed the structure of the 12RSS in the SC and PC using fluorescence resonance energy transfer (FRET) and molecular dynamics modeling. The resulting models indicate that the 12RSS adopts a strongly bent V-shaped structure upon RAG/HMGB1 binding and reveal structural differences, particularly near the heptamer, between the 12RSS in the SC and PC. Comparison of models of the 12RSS and 23RSS in the PC reveals broadly similar shapes but a distinct number and location of DNA bends as well as a smaller central cavity for the 12RSS. These findings provide the most detailed view yet of the 12RSS in RAG–DNA complexes and highlight structural features of the RSS that might underlie activation of RAG-mediated cleavage and substrate asymmetry important for the 12/23 rule of V(D)J recombination.