Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA

Diges, C. M.

doi:10.1093/emboj/20.19.5503

Cited by 138 publications

(202 citation statements)

References 54 publications

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“…Our lack of knowledge about RNA-binding sites has prevented us from establishing complete physical models for how DEAD box proteins function and has precluded further elucidation of whether and how these helicases alter RNA structures. So far, exact RNA-binding sites are known only for eIF4AIII, in the context of the EJC 69 , and for bacterial DbpA and its orthologues, which bind with high affinity to a ribosomal RNA hairpin 138 . The vast majority of DEAD box proteins lack inherent substrate specificity, and physiological RNA binding sites need to be explicitly determined.…”

Section: Future Challenges and Perspectivementioning

confidence: 99%

From unwinding to clamping — the DEAD box RNA helicase family

Linder

Jankowsky

2011

Nat Rev Mol Cell Biol

990

1,069

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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: Future Challenges and Perspectivementioning

confidence: 99%

From unwinding to clamping — the DEAD box RNA helicase family

Linder

Jankowsky

2011

Nat Rev Mol Cell Biol

990

1,069

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“…For example, the C-terminal domains of the splicing helicases CYT-19 and Mss116 mediates interactions with structured RNA (Grohman et al, 2007;Mohr et al, 2008). In contrast, the C-terminal domains of DbpA and YxiN specifically interact with a hairpin in ribosomal RNA (Diges and Uhlenbeck, 2001;Tsu et al, 2001;Kossen et al, 2002;Karginov et al, 2005;Wang et al, 2006), and the C-terminal domain of Hera provides high affinity for ribosomal RNA and RNase P RNA, among others (Morlang et al, 1999;Linden et al, 2008). The influence of domains flanking the helicase core on RNA binding and on DEAD box mechanism in general will be discussed in detail in 'Modulation of the helicase core activity by interacting partners and flanking domains'.…”

Section: Rna Bindingmentioning

confidence: 99%

“…Although different unwinding activities of DEAD box proteins for duplexes with 59-or 39-single stranded overhangs have been reported, this 'directionality' possibly reflects differences in unwinding that depend on the relative orientation of the DEAD box protein with regard to the target region. For example, the Cterminal domain of DbpA recognizes a hairpin in ribosomal 23S rRNA and the helicase core unwinds an adjacent helix (Fuller-Pace et al, 1993;Diges and Uhlenbeck, 2001;Tsu et al, 2001). Unwinding efficiencies depend on the position of the helix relative to the hairpin (Diges and Uhlenbeck, 2005).…”

Section: Characteristics Of Rna Helicase Substratesmentioning

confidence: 99%

“…ATP hydrolysis is required to reset the enzyme to a low-affinity state for RNA and to allow for multiple rounds of unwinding (Chen et al, 2008). For DEAD box proteins with additional RNA binding domains, the helicase core might remain tethered to the RNA substrate, allowing for multiple catalytic cycles (Diges and Uhlenbeck, 2001;Tijerina et al, 2006). Remodeling of RNP complexes can be rationalized by the same mechanism and would be a consequence of local distortions of the RNA that interfere with protein binding.…”

Section: A Unifying Mechanism For Dead Box Protein Activity?mentioning

confidence: 99%

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

Hilbert

Karow²,

Klostermeier³

2009

BCHM

143

171

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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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“…The DbpA protein is famous for its requirement for a specific RNA substrate for efficient ATP hydrolysis (Fuller-Pace et al, 1993). Indeed, this DEAD-box protein is exclusively and heavily stimulated in its activity by the hairpin h92 from the 23S rRNA (Diges and Uhlenbeck, 2001;Nicol and Fuller-Pace, 1995). Recently, it was shown that a dominant-negative mutation in motif VI of dbpA results in a ribosome biogenesis defect (Elles and Uhlenbeck, 2008).…”

Section: Introductionmentioning

confidence: 99%