Lomakin Ivan B, De Swastik, Wang Jimin, Borkar Aditi N, Steitz Thomas A
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
Comput Struct Biotechnol J. 2020 Mar 19;18:696-704. doi: 10.1016/j.csbj.2020.03.009. eCollection 2020.
The density regulated protein (DENR) forms a stable heterodimer with malignant T-cell-amplified sequence 1 (MCT-1). DENR-MCT-1 heterodimer then participates in regulation of non-canonical translation initiation and ribosomal recycling. The N-terminal domain of DENR interacts with MCT-1 and carries a classical tetrahedral zinc ion-binding site, which is crucial for the dimerization. DENR-MCT-1 binds the small (40S) ribosomal subunit through interactions between MCT-1 and helix h24 of the 18S rRNA, and through interactions between the C-terminal domain of DENR and helix h44 of the 18S rRNA. This later interaction occurs in the vicinity of the P site that is also the binding site for canonical translation initiation factor eIF1, which plays the key role in initiation codon selection and scanning. Sequence homology modeling and a low-resolution crystal structure of the DENR-MCT-1 complex with the human 40S subunit suggests that the C-terminal domain of DENR and eIF1 adopt a similar fold. Here we present the crystal structure of the C-terminal domain of DENR determined at 1.74 Å resolution, which confirms its resemblance to eIF1 and advances our understanding of the mechanism by which DENR-MCT-1 regulates non-canonical translation initiation and ribosomal recycling.
密度调节蛋白（DENR）与恶性T细胞扩增序列1（MCT-1）形成稳定的异二聚体。DENR-MCT-1异二聚体随后参与非经典翻译起始和核糖体循环的调控。DENR的N端结构域与MCT-1相互作用，并带有一个经典的四面体锌离子结合位点，这对于二聚化至关重要。DENR-MCT-1通过MCT-1与18S rRNA的h24螺旋之间的相互作用，以及DENR的C端结构域与18S rRNA的h44螺旋之间的相互作用，结合小（40S）核糖体亚基。后一种相互作用发生在P位点附近，P位点也是经典翻译起始因子eIF1的结合位点，eIF1在起始密码子选择和扫描中起关键作用。DENR-MCT-1与人类40S亚基复合物的序列同源性建模和低分辨率晶体结构表明，DENR的C端结构域和eIF1具有相似的折叠。在此，我们展示了以1.74 Å分辨率测定的DENR C端结构域的晶体结构，这证实了它与eIF1的相似性，并加深了我们对DENR-MCT-1调控非经典翻译起始和核糖体循环机制的理解。
