Comparative structural analyses and nucleotide-binding characterization of the four KH domains of FUBP1
Comparative structural analyses and nucleotide-binding characterization of the four KH domains of FUBP1
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DOI：
10.1038/s41598-020-69832-z
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发表时间：
2020-08-10
影响因子：
4.6
通讯作者：
Chaikuad, Apirat
中科院分区：
文献类型：
--
作者：
Ni, Xiaomin;Knapp, Stefan;Chaikuad, Apirat
FUBP 1-FUSE复合物是转录分子机制的重要组成部分，其对于包括c-Myc和p21在内的许多关键基因的表达的严格调节是必需的。FUBP 1利用其四个铰接的KH模块，其协同作用，用于FUSE核苷酸结合。为了了解分子间相互作用的分子机制，我们提出了一组晶体结构，以及FUBP 1 KH结构域的ssDNA结合特性。所有KH 1 -4基序在拓扑结构上高度保守，并且能够单独和独立地与FUSE相互作用。然而，四个KH结构域之间的核苷酸结合特性的差异是明显的，包括更高的核苷酸结合效力的KH 3以及不同的核苷酸序列的偏好。在负责核碱基的结合裂缝的一侧的氨基酸组成的变化导致不同的形状和静电荷相互作用，这可能是可行的一个促成因素，不同的核苷酸之间的结合倾向KH 1 -4。尽管如此，在所有四个KH基序的结构和核苷酸结合特性的保护是必不可少的FUBP 1中存在的多KH模块对FUSE相互作用的纳摩尔亲和力的协同性。全面的结构比较和ssDNA结合特性的所有四个KH结构域在这里提供了一个基本的水平，可能是有益的阐明FUBP 1-FUSE相互作用的机制的分子见解。
The FUBP1-FUSE complex is an essential component of a transcription molecular machinery that is necessary for tight regulation of expression of many key genes including c-Myc and p21. FUBP1 utilizes its four articulated KH modules, which function cooperatively, for FUSE nucleotide binding. To understand molecular mechanisms fundamental to the intermolecular interaction, we present a set of crystal structures, as well ssDNA-binding characterization of FUBP1 KH domains. All KH1-4 motifs were highly topologically conserved, and were able to interact with FUSE individually and independently. Nevertheless, differences in nucleotide binding properties among the four KH domains were evident, including higher nucleotide-binding potency for KH3 as well as diverse nucleotide sequence preferences. Variations in amino acid compositions at one side of the binding cleft responsible for nucleobase resulted in diverse shapes and electrostatic charge interaction, which might feasibly be a contributing factor for different nucleotide-binding propensities among KH1-4. Nonetheless, conservation of structure and nucleotide-binding property in all four KH motifs is essential for the cooperativity of multi KH modules present in FUBP1 towards nanomolar affinity for FUSE interaction. Comprehensive structural comparison and ssDNA binding characteristics of all four KH domains presented here provide molecular insights at a fundamental level that might be beneficial for elucidating the mechanisms of the FUBP1-FUSE interaction.