The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X

• Published in: Nature communications Vol. 10; no. 1; pp. 3085 - 8
• Main Authors: Song, He, Ji, Xinhua
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 12-07-2019; Nature Publishing Group; Nature Portfolio
• Subjects: 631/337/1645; 631/45/173; 631/535/1261; 631/535/1266; ATP; BASIC BIOLOGICAL SCIENCES; Cancer; Crystal structure; DEAD-box RNA Helicases - isolation & purification; DEAD-box RNA Helicases - metabolism; DEAD-box RNA Helicases - ultrastructure; DNA helicase; Domains; Double-stranded RNA; enzyme mechanisms; Humanities and Social Sciences; Metabolism; multidisciplinary; Polypeptides; RecA protein; Recombinant Proteins - isolation & purification; Recombinant Proteins - metabolism; Recombinant Proteins - ultrastructure; RNA metabolism; RNA processing; RNA, Double-Stranded - metabolism; SAXS; Scattering, Small Angle; Science; Science (multidisciplinary); Substrate Specificity; Unwinding; x-ray crystallography; X-Ray Diffraction
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-11083-2

DEAD-box helicases (DDXs) regulate RNA processing and metabolism by unwinding short double-stranded (ds) RNAs. Sharing a helicase core composed of two RecA-like domains (D1D2), DDXs function in an ATP-dependent, non-processive manner. As an attractive target for cancer and AIDS treatment, DDX3X and its orthologs are extensively studied, yielding a wealth of biochemical and biophysical data, including structures of apo-D1D2 and post-unwound D1D2:single-stranded RNA complex, and the structure of a D2:dsRNA complex that is thought to represent a pre-unwound state. However, the structure of a pre-unwound D1D2:dsRNA complex remains elusive, and thus, the mechanism of DDX action is not fully understood. Here, we describe the structure of a D1D2 core in complex with a 23-base pair dsRNA at pre-unwound state, revealing that two DDXs recognize a 2-turn dsRNA, each DDX mainly recognizes a single RNA strand, and conformational changes induced by ATP binding unwinds the RNA duplex in a cooperative manner.
DEAD-box helicases (DDXs) function in an ATP-dependent, non-processive manner and the conserved helicase core is composed of two RecA-like domains D1 and D2. Here the authors present the crystal structure of the D1D2 core from human DDX3X bound to a 23-base pair dsRNA in the pre-unwound state and discuss the implications for helicase mechanism.