Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2
Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2
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DOI：
10.1093/nar/gky1302
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发表时间：
2019-04-08
影响因子：
14.9
通讯作者：
Hamdane, Djemel
中科院分区：
文献类型：
--
作者：
Bou-Nader, Charles;Barraud, Pierre;Hamdane, Djemel
双链RNA结合结构域（dsRBD）是一种广泛存在的特异性识别双链RNA的结构域。dsRBD存在于参与RNA代谢的各种功能作用（包括RNA剪接、编辑和转运）的许多蛋白质和酶中，通常与缺乏复杂结构的RNA结合。然而，这种信念最近受到了挑战，发现了一个dsRBD作为一个主要的tRNA结合模块的人二氢尿苷合酶2（hDus 2），黄素酶，催化合成二氢尿苷内的复杂的肘状结构的tRNA。我们在这里揭示了hDus 2 dsRBD识别tRNA配体的分子机制。通过解决这种dsRBD与dsRNA复合的晶体结构，以及使用诱变、NMR和SAXS对其与tRNA相互作用的广泛表征，我们确定，虽然hDus 2 dsRBD保留了常规的dsRNA识别能力，但附加到典型结构域的N-末端延伸的存在提供了用于以结构特异性作用模式结合tRNA的额外残基。我们的研究结果支持，这种扩展代表了dsRBD专门从事tRNA生物学的功能，并更广泛地强调了典型结构域的结构附件在促进功能多样性出现方面的重要性。
Double stranded RNA-binding domain (dsRBD) is a ubiquitous domain specialized in the recognition of double-stranded RNAs (dsRNAs). Present in many proteins and enzymes involved in various functional roles of RNA metabolism, including RNA splicing, editing, and transport, dsRBD generally binds to RNAs that lack complex structures. However, this belief has recently been challenged by the discovery of a dsRBD serving as a major tRNA binding module for human dihydrouridine synthase 2 (hDus2), a flavoenzyme that catalyzes synthesis of dihydrouridine within the complex elbow structure of tRNA. We here unveil the molecular mechanism by which hDus2 dsRBD recognizes a tRNA ligand. By solving the crystal structure of this dsRBD in complex with a dsRNA together with extensive characterizations of its interaction with tRNA using mutagenesis, NMR and SAXS, we establish that while hDus2 dsRBD retains a conventional dsRNA recognition capability, the presence of an N-terminal extension appended to the canonical domain provides additional residues for binding tRNA in a structure-specific mode of action. Our results support that this extension represents a feature by which the dsRBD specializes in tRNA biology and more broadly highlight the importance of structural appendages to canonical domains in promoting the emergence of functional diversity.