Jawed vertebrate adaptive immunity relies on the RAG1/RAG2 (RAG) recombinase, a domesticated transposase, for assembly of antigen receptor genes. Using an integration‐activated form of RAG1 with methionine at residue 848 and cryo‐electron microscopy, we determined structures that capture RAG engaged with transposon ends and U‐shaped target DNA prior to integration (the target capture complex) and two forms of the RAG strand transfer complex that differ based on whether target site DNA is annealed or dynamic. Target site DNA base unstacking, flipping, and melting by RAG1 methionine 848 explain how this residue activates transposition, how RAG can stabilize sharp bends in target DNA, and why replacement of residue 848 by arginine during RAG domestication led to suppression of transposition activity. RAG2 extends a jawed vertebrate‐specific loop to interact with target site DNA, and functional assays demonstrate that this loop represents another evolutionary adaptation acquired during RAG domestication to inhibit transposition. Our findings identify mechanistic principles of the final step in cut‐and‐paste transposition and the molecular and structural logic underlying the transformation of RAG from transposase to recombinase.

中文翻译：

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RAG 重组酶进化过程中转座激活和抑制的结构基础。

下颌脊椎动物适应性免疫依赖于 RAG1/RAG2 (RAG) 重组酶，一种驯化的转座酶，用于抗原受体基因的组装。使用整合激活形式的 RAG1 与残基 848 处的甲硫氨酸和冷冻电子显微镜，我们确定了在整合之前捕获与转座子末端和 U 形目标 DNA 接合的 RAG 的结构（目标捕获复合物）和两种形式的 RAG链转移复合物根据目标位点 DNA 是退火的还是动态的而有所不同。RAG1 甲硫氨酸 848 对目标位点 DNA 碱基的分解、翻转和熔化解释了该残基如何激活转座，RAG 如何稳定目标 DNA 中的急剧弯曲，以及为什么在 RAG 驯化过程中用精氨酸替换残基 848 导致转座活性受到抑制。RAG2 扩展了一个有颚脊椎动物特异性环以与目标位点 DNA 相互作用，功能分析表明该环代表了在 RAG 驯化过程中获得的另一种进化适应，以抑制转座。我们的研究结果确定了剪切和粘贴转座最后一步的机械原理，以及 RAG 从转座酶转化为重组酶的分子和结构逻辑。