Abstract
RNA helicase DDX21 plays vital roles in ribosomal RNA biogenesis, transcription, and the regulation of host innate immunity during virus infection. How DDX21 recognizes and unwinds RNA and how DDX21 interacts with virus remain poorly understood. Here, crystal structures of human DDX21 determined in three distinct states are reported, including the apo‐state, the AMPPNP plus single‐stranded RNA (ssRNA) bound pre‐hydrolysis state, and the ADP‐bound post‐hydrolysis state, revealing an open to closed conformational change upon RNA binding and unwinding. The core of the RNA unwinding machinery of DDX21 includes one wedge helix, one sensor motif V and the DEVD box, which links the binding pockets of ATP and ssRNA. The mutant D339H/E340G dramatically increases RNA binding activity. Moreover, Hill coefficient analysis reveals that DDX21 unwinds double‐stranded RNA (dsRNA) in a cooperative manner. Besides, the nonstructural (NS1) protein of influenza A inhibits the ATPase and unwinding activity of DDX21 via small RNAs, which cooperatively assemble with DDX21 and NS1. The structures illustrate the dynamic process of ATP hydrolysis and RNA unwinding for RNA helicases, and the RNA modulated interaction between NS1 and DDX21 generates a fresh perspective toward the virus–host interface. It would benefit in developing therapeutics to combat the influenza virus infection.
Highlights
DExD/H-box RNA helicases unwind RNA structures or dissociate RNA-protein complexes in cellular processes that require modulation of RNA structures.[1]
Crystal structure of DDX21 with an ADP molecule was solved at 2.7 Å; one internal loop was disordered, and the ADP molecule for crystallization was spontaneously hydrolyzed into AMP (Figure 1E)
The DDX21-AMPPNP-single-stranded RNA (ssRNA) ternary complex structure contained two molecules in the asymmetric unit, named as A chain and B chain, respectively, which bound to a poly(U) mRNA mimic, a non-hydrolyzable nucleotide AMPPNP, and one Mg2+ ion
Summary
DExD/H-box RNA helicases unwind RNA structures or dissociate RNA-protein complexes in cellular processes that require modulation of RNA structures.[1]. They are vital for the regulation of all aspects of the RNA life cycle, including premRNA splicing, mRNA export, RNA editing, storage and decay, ribosome biogenesis, and transcription,[2] as well as participating in the regulation of protein translation modification,[3] cellular signaling pathways,[4] and protein localization.[5]. Many DExD-box helicases exhibit essential functions in innate immunity,[6] as well as associated with multiple kinds of cancers,[7] making the helicases attractive therapeutic targets and potential biomarkers for cancer diagnosis, prognosis, and therapeutics. RNA helicase DDX21 contains all signature motifs of the DExD-box helicase family and three atypical FRGQR repeats and one PRGQR motif (Figure 1A).[8].
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