The DEXD/H-box RNA Helicase DDX19 Is Regulated by an α-Helical Switch

Collins, R.; Karlberg, T.; Lehtiö, L.; Schutz, P.; Berg, S. Van Den; Dahlgren, Lars; Hammarstrom, M.; Weigelt, J.; Schüler, H.

doi:10.1074/jbc.c900018200

Cited by 124 publications

(176 citation statements)

References 28 publications

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“…The structure and the biochemical analysis of the mammalian homologue of Dbp5, DDX19, reveal an interesting potential mode of self-regulation 119 . In this analysis, it was shown that the sequence that lies just to the N-terminal side of the Q-motif of DDX19 inhibit s ATP hydrolysis, by competing with the Arg finger (motif VI), unless this extension becomes displaced by RNA.…”

Section: Nuclear Specklesmentioning

confidence: 99%

From unwinding to clamping — the DEAD box RNA helicase family

Linder

Jankowsky

2011

Nat Rev Mol Cell Biol

917

1,040

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Nearly all aspects of RNA metabolism, from transcription and translation to mRNA decay, involve RNA helicases, which are enzymes that use ATP to bind or remodel RNA and RNA-protein complexes (ribonucleoprotein (RNP) complexes) 1 . RNA helicases are found in all three domains of life, and many viruses also encode one or more of these proteins 2,3 . Together with the structurally related DNA helicases that function in replication, recombination and repair, the RNA helicases are classified into superfamilies and families, based on sequence and structural features 3,4 . DEAD box proteins form the largest helicase family, with 37 members in humans and 26 in Saccharomyces cerevisiae 3 , and are characterized by the presence of an Asp-Glu-Ala-Asp (DEAD) motif.DEAD box helicases have central and, in many cases, essential physiological roles in cellular RNA metabolism 5 (FIG. 1). The proteins generally function as part of larger multicomponent assemblies, such as the spliceosom e or the eukaryotic translation initiation machinery 6 . Mutations and deregulation of several DEAD box proteins have been linked to disease states, including cancer 7 . Although all DEAD box proteins contain a structurally highly conserved core with conserved ATP-binding and RNA-binding sites, different proteins have been associated with diverse and seemingly unrelated functions, including the disassembly of RNPs, chaperoning during RNA folding and even stabil ization of protein complexes on RNA 5,6 . How these highly conserved proteins fulfil such an array of different functions has been a long-standing question.Research has now started to illuminate the molecular basis for this functional diversity. In this Review, we summarize how structural data, together with biochemical and biophysical studies, have revealed unexpected modes by which these proteins function. We also discuss how novel molecular and cell biological approaches have better defined the cellular roles of DEAD box helicases. We outline our current view on common structural and mechan istic themes that have emerged, and on physical models of how these 'unusual' RNA helicases work.Structures of DEAD box RNA helicases A number of structural studies have universally shown that members of the DEAD box family contain a highly conserved helicase core that harbours the binding sites for ATP and RNA 3,4,8 . The core is surrounded by variable auxiliary domains, which are thought to be critical for the diverse functions of these enzymes.Structure of the helicase core. DEAD box proteins belong to helicase superfamily 2 (SF2) 2 . Similarly to all SF2 helicases, DEAD box proteins are built around a highly conserved helicase core of two virtually identical domains that resemble the bacterial recombination protein recombinase A (RecA) 3,4,8 (FIG. 2a,b). Within this helicase core, at least 12 characteristic sequence motifs are located at conserved positions (FIG. 2a,b). Some of these motifs are conserved across the entire SF2 family, whereas others are found only in the DEAD box family 3 ....

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Section: Nuclear Specklesmentioning

confidence: 99%

From unwinding to clamping — the DEAD box RNA helicase family

Linder

Jankowsky

2011

Nat Rev Mol Cell Biol

917

1,040

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“…When overall RNA affinities are determined, nucleotide-dependent substrate binding properties of the core will thus be masked by the nucleotideindependent high RNA affinity of the flanking domain, and it is crucial to dissect the individual contributions. Recent evidence suggests that additional domains can also influence nucleotide binding (Collins et al, 2009;Fan et al, 2009;Napetschnig et al, 2009;von Moeller et al, 2009), see also the section on 'modulation of the helicase core activity by interacting partners and flanking domains'.…”

Section: Interaction Of Dead Box Proteins With Adenine Nucleotides Anmentioning

confidence: 99%

“…The RNA binding site of the helicase core is formed by both RecA-like domains, and binding involves contacts to motifs Ia, GG, and Ib in the N-terminal domain, and to motifs IV, QxxR, V, and VI in the C-terminal domain (Pause et al, 1993;Andersen et al, 2006;Bono et al, 2006;Sengoku et al, 2006;Nielsen et al, 2008;Collins et al, 2009;von Moeller et al, 2009) (Figures 1 and 3B). In all available structures, the N-terminal RecA-like domain binds the 39-region of the ssRNA substrate, and the C-terminal domain binds the 59-region.…”

Section: Rna Bindingmentioning

confidence: 99%

“…Structural studies have provided a first glimpse on the individual interactions between the conserved motifs in the absence or presence of ATP and ssRNA substrate (Caruthers et al, 2000;Story et al, 2001;Cheng et al, 2005;Andersen et al, 2006;Bono et al, 2006;Sengoku et al, 2006;Nielsen et al, 2008;Collins et al, 2009;von Moeller et al, 2009). When both substrates are bound, the helicase motifs engage in a complex network with a multitude of cooperative interactions, complicating the assignment of functional contributions for each individual motif in mutagenesis studies (Banroques et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…No nucleotide binding is observed when the two RecA-like domains are mixed without a covalent linkage (Karow et al, 2007), confirming that interactions between these domains are weak. In contrast to the open conformation in the absence of ligands, the helicase core of DEAD box proteins adopts a compact, closed conformation in the presence of ssRNA and nucleotide, as exemplified by the crystal structures of the DEAD box proteins eIF4A-III, Vasa, and Ddx19 in complex with ssRNA and the non-hydrolyzable ATP-analog ADPNP (Andersen et al, 2006;Bono et al, 2006;Sengoku et al, 2006;Collins et al, 2009;von Moeller et al, 2009; Figure 2B). In these structures, most of the conserved motifs face the interdomain cleft between the RecA-like domains and are engaged in a complex hydrogen bond network.…”

Section: Introductionmentioning

confidence: 99%

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The mechanism of ATP-dependent RNA unwinding by DEAD box proteins

Hilbert

Karow²,

Klostermeier³

2009

BCHM

133

168

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DEAD box proteins catalyze the ATP-dependent unwinding of double-stranded RNA (dsRNA). In addition, they facilitate protein displacement and remodeling of RNA or RNA/protein complexes. Their hallmark feature is local destabilization of RNA duplexes. Here, we summarize current data on the DEAD box protein mechanism and present a model for RNA unwinding that integrates recent data on the effect of ATP analogs and mutations on DEAD box protein activity. DEAD box proteins share a conserved helicase core with two flexibly linked RecAlike domains that contain all helicase signature motifs. Variable flanking regions contribute to substrate binding and modulate activity. In the presence of ATP and RNA, the helicase core adopts a compact, closed conformation with extensive interdomain contacts and high affinity for RNA. In the closed conformation, the RecA-like domains form a catalytic site for ATP hydrolysis and a continuous RNA binding site. A kink in the backbone of the bound RNA locally destabilizes the duplex. Rearrangement of this initial complex generates a hydrolysisand unwinding-competent state. From this complex, the first RNA strand can dissociate. After ATP hydrolysis and phosphate release, the DEAD box protein returns to a low-affinity state for RNA. Dissociation of the second RNA strand and reopening of the cleft in the helicase core allow for further catalytic cycles.

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Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation

Chen

et al. 2020

Advanced Science

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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.

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The DEXD/H-box RNA Helicase DDX19 Is Regulated by an α-Helical Switch

Cited by 124 publications

References 28 publications

From unwinding to clamping — the DEAD box RNA helicase family

From unwinding to clamping — the DEAD box RNA helicase family

The mechanism of ATP-dependent RNA unwinding by DEAD box proteins

Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation

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