DEPTOR is an inhibitor of the mTOR kinase which controls cell growth. DEPTOR consists of two DEP domains and a PDZ domain connected by an unstructured linker, and its stability is tightly regulated through post-translational modifications of its linker region that contains the ²⁸⁶SSGYFS²⁹¹ degron. Based on the mTORC1 complex, our modelling suggests a possible spatial arrangement of DEPTOR which is characterised to form a dimer. Our model shows that the two PDZ domains of a DEPTOR dimer bind separately to the dimeric mTOR’s FAT domains ~130 Å apart, while each of the two extended linkers is sufficiently long to span from the FAT domain to the kinase domain of mTOR and beyond to join a shared dimer of the DEP domains. This places the linker’s S299 closest to the kinase’s catalytic site, indicating that phosphorylation would start with it and successively upstream towards DEPTOR’s degron. The CK1α kinase is reportedly responsible for the phosphorylation of the degron, and our docking analysis further reveals that CK1α contains sites to bind DEPTOR’s pS286, pS287 and pT295, which may act as priming phosphates for the phosphorylation of the degron’s S291. DEPTOR’s linker can also be ubiquitylated by the UbcH5A–SCF^β-TrCP complex without its PDZ dissociating from mTOR according to the modelling. As the catalytic cleft of mTOR’s kinase is restricted, interactions between the kinase’s unstructured segment surrounding the cleft and DEPTOR’s linker, which may involve S293 and S299, may be critical to controlling DEPTOR’s access to the catalytic cleft and hence its phosphorylation by mTOR in a manner dependent on mTOR’s activation.

DEPTOR 是控制细胞生长的 mTOR 激酶抑制剂。DEPTOR 由两个 DEP 域和一个由非结构化接头连接的 PDZ 域组成，其稳定性通过其包含²⁸⁶ SSGYFS ^{291 的}接头区域的翻译后修饰受到严格调控德格龙。基于 mTORC1 复合物，我们的建模表明了 DEPTOR 的可能空间排列，其特征在于形成二聚体。我们的模型显示 DEPTOR 二聚体的两个 PDZ 域分别与二聚体 mTOR 的 FAT 域相距约 130 Å 结合，而两个扩展接头中的每一个都足够长，可以从 FAT 域跨越到 mTOR 的激酶域，甚至更远加入 DEP 域的共享二聚体。这将连接器的 S299 放置在最靠近激酶催化位点的位置，表明磷酸化将从它开始，并连续向 DEPTOR 的 degron 上游。据报道，CK1 α激酶负责 degron 的磷酸化，我们的对接分析进一步表明 CK1 α包含结合 DEPTOR 的 pS286、pS287 和 pT295 的位点，这些位点可以作为 degron 的 S291 磷酸化的引发磷酸盐。根据模型，DEPTOR 的接头也可以被 UbcH5A-SCF ^β - ^TrCP复合物泛素化，而其 PDZ 不会与 mTOR 分离。由于 mTOR 激酶的催化裂隙受到限制，裂隙周围激酶的非结构化片段与 DEPTOR 的接头（可能涉及 S293 和 S299）之间的相互作用对于控制 DEPTOR 进入催化裂隙并因此以某种方式被 mTOR 磷酸化可能是至关重要的依赖于 mTOR 的激活。