GapR is a nucleoid-associated protein that is an essential regulator of chromosome replication in the cell cycle model Caulobacter crescentus. Here, we demonstrate that free GapR is a homotetramer, but not a dimer as previously reported (Guo et al., Cell 175: 583–597, 2018). We have determined the crystal structure of GapR in complex with a 10-bp A-tract DNA, which has an open tetrameric conformation, different from the closed clamp conformation in the previously reported crystal structure of GapR/DNA complex. The free GapR adopts multiple conformations in dynamic exchange equilibrium, with the major conformation resembling the closed tetrameric conformation, while the open tetrameric conformation is a representative of minor conformers. As it is impossible for the circular genomic DNA to get into the central DNA binding tunnel of the major conformation, we propose that GapR initially binds DNA through the open conformation, and then undergoes structural rearrangement to form the closed conformation which fully encircles the DNA. GapR prefers to bind DNA with 10-bp consecutive A/T base pairs nonselectively (K_d ∼12 nM), while it can also bind GC-rich DNA sequence with a reasonable affinity of about 120 nM. Besides, our results suggest that GapR binding results in widening the minor groove of AT-rich DNA, instead of overtwisting DNA.

中文翻译：

---

GapR通过动态打开其四聚体界面结合DNA。

GapR是一种与核苷相关的蛋白，是细胞周期新月形杆菌中染色体复制的重要调节剂。在这里，我们证明了游离GapR是同型四聚体，而不是先前报道的二聚体（Guo等。，Cell 175：583-597，2018年）。我们已经确定了具有10 bp A链DNA的复合物中GapR的晶体结构，该DNA具有开放的四聚体构象，不同于先前报道的GapR / DNA复合物的晶体结构中的封闭钳构象。游离GapR在动态交换平衡中采用多种构象，主要构象类似于封闭的四聚体构象，而开放的四聚体构象是次要构象的代表。由于环状基因组DNA不可能进入主要构象的中央DNA结合通道，我们建议GapR首先通过开放构象结合DNA，然后进行结构重排以形成完全包围DNA的封闭构象。ķ _d〜12 nM）的，虽然它也可以绑定与约120 nM的亲和力合理富含GC的DNA序列。此外，我们的结果表明，GapR结合会导致富含AT的DNA的小沟变宽，而不是使DNA过度扭曲。