Crystal structure of a DEAD box protein from the hyperthermophile
            <i>Methanococcus jannaschii</i>

Story, Randall M.; Li, Hong; Abelson, John

doi:10.1073/pnas.98.4.1465

Cited by 138 publications

(156 citation statements)

References 42 publications

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“…Crystal structures of various DEAD box proteins without ligands show a large variety of relative orientations of the two RecA-like domains ( Figure 2A; Caruthers et al, 2000;Story et al, 2001;Cheng et al, 2005;Andersen et al, 2006) and point to a significant flexibility that is presumably provided by the linker region. Solution studies of the Bacillus subtilis DEAD box protein YxiN are in agreement with such a high flexibility.…”

Section: Introductionmentioning

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%

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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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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Hilbert

Karow²,

Klostermeier³

2009

BCHM

143

171

View full text Add to dashboard Cite

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“…As the conserved motifs necessary for ATP binding and hydrolysis are contained within the N-terminal domain, the structure of BstDEAD-NT is expected to be similar to the corresponding ATPase domains of other DEAD proteins. A structural relatedness search performed with DALI (Holm and Sander 1993) identified similarity with a large number of proteins possessing ATPase domains, the most closely related of which are the ATPase (N-terminal) domains of eIF4A (Caruthers et al 2000) and mjDEAD (Story et al 2001), with 199 C␣ positions that superimpose with a root mean square difference (RMSD) of 1.3Å and 1.4Å, respectively. An overlay of these structures is shown in FIGURE 2.…”

Section: Relationship To Other Proteinsmentioning

confidence: 99%

“…As seen in Figure 1A, the loop connecting the two N-terminal helices contains the Q-motif, a recently identified stretch of highly conserved amino acid residues unique to the DEAD protein family (Tanner et al 2003). In the crystal structures of eIF4A and mjDEAD (Caruthers et al 2000;Story et al 2001), as in the putative structure of full-length Bst-DEAD, the ␤7 strand leads into the flexible polypeptide linker that connects the two core domains. In addition to the Q-motif, the N-terminal domain contains the conserved helicase motifs I, II, and III that are responsible for binding and hydrolysis of ATP plus motifs Ia and Ib that play poorly defined roles in substrate recognition.…”

Section: Structure Of the N-terminal Domain (Bstdead-nt)mentioning

confidence: 99%

“…Despite the fact that the number of DEAD proteins identified by sequence homology is large, the biological functions of most of these proteins remain unknown. Furthermore, high-resolution structures remain limited to two DEAD proteins, yeast eIF4A and mjDEAD from Methanococcus janaschii (Caruthers et al 2000;Story et al 2001), and the HCV helicase, a DExH protein from hepatitis C (Kim et al 1998). …”

Section: Introductionmentioning

confidence: 99%

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Crystal structure of the BstDEAD N-terminal domain: A novel DEAD protein from Bacillus stearothermophilus

Carmel

Matthews²

2003

RNA

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Most cellular processes requiring RNA structure rearrangement necessitate the action of Asp-Glu-Ala-Asp (DEAD) proteins. Members of the family, named originally for the conserved DEAD amino acid sequence, are thought to disrupt RNA structure and facilitate its rearrangement by unwinding short stretches of duplex RNA. BstDEAD is a novel 436 amino acid representative of the DEAD protein family from Bacillus stearothermophilus that contains all eight conserved motifs found in DEAD proteins and is homologous with other members of the family. Here, we describe the 1.85 Å resolution structure of the N-terminal domain (residues 1-211) of BstDEAD (BstDEAD-NT). Similar to the corresponding domains of related helicases, BstDEAD-NT adopts a parallel ␣/␤ structure with RecA-like topology. In general, the conserved motifs superimpose on closely related DEAD proteins and on more distantly related helicases such as RecA. This affirms the current belief that the core helicase domains, responsible for mechanistic activity, are structurally similar in DEAD proteins. In contrast, however, the so-called Walker A P-loop, which binds the ␤-and ␥-phosphates of ATP, adopts a rarely seen "closed" conformation that would sterically block ATP binding. The closed conformation may be indicative of a general regulatory feature among DEAD proteins (and RNA helicases) that differs from that used by DNA helicases. BstDEAD also contains a unique extension of ∼ 60 residues at the C terminus that is highly basic, suggesting that it might bind nucleic acids and, in so doing, confer specificity to the helicase activity of the core region.

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Mutational analysis of the functional motifs of the DEAD‐box RNA helicase Me31B/DDX6 in Drosophila germline development

et al. 2023

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Me31B/DDX6 is a DEAD-box family RNA helicase playing roles in posttranscriptional RNA regulation in different cell types and species. Despite the known motifs/domains of Me31B, the in vivo functions of the motifs remain unclear. Here, we used the Drosophila germline as a model and used CRISPR to mutate the key Me31B motifs/domains: helicase domain, N-terminal domain, C-terminal domain and FDF-binding motif. Then, we performed screening characterization on the mutants and report the effects of the mutations on the Drosophila germline, on processes such as fertility, oogenesis, embryo patterning, germline mRNA regulation and Me31B protein expression. The study indicates that the Me31B motifs contribute different functions to the protein and are needed for proper germline development, providing insights into the in vivo working mechanism of the helicase.

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Crystal structure of a DEAD box protein from the hyperthermophile Methanococcus jannaschii

Cited by 138 publications

References 42 publications

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

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

Crystal structure of the BstDEAD N-terminal domain: A novel DEAD protein from Bacillus stearothermophilus

Mutational analysis of the functional motifs of the DEAD‐box RNA helicase Me31B/DDX6 in Drosophila germline development

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